amplicon_analysis_pipeline: install_tool

annotate install_tool_deps.sh @ 37:e832be1635b4 draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 601f7d1e21b25c583cc6e1a563029bab3f226921-dirty

author	pjbriggs
date	Tue, 16 Oct 2018 10:54:44 -0400
parents	013bf1e2cc8f
children

rev	line source
0 b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	1 #!/bin/bash -e
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	2 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	3 # Install the tool dependencies for Amplicon_analysis_pipeline.sh for
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	4 # testing from command line
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	5 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	6 function install_python_package() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	7 echo Installing $2 $3 from $4 under $1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	8 local install_dir=$1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	9 local install_dirs="$install_dir $install_dir/bin $install_dir/lib/python2.7/site-packages"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	10 for d in $install_dirs ; do
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	11 if [ ! -d $d ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	12 mkdir -p $d
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	13 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	14 done
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	15 wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	16 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	17 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	18 wget -q $4
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	19 if [ ! -f "$(basename $4)" ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	20 echo "No archive $(basename $4)"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	21 exit 1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	22 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	23 tar xzf $(basename $4)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	24 if [ ! -d "$5" ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	25 echo "No directory $5"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	26 exit 1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	27 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	28 cd $5
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	29 /bin/bash <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	30 export PYTHONPATH=$install_dir:$PYTHONPATH && \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	31 export PYTHONPATH=$install_dir/lib/python2.7/site-packages:$PYTHONPATH && \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	32 python setup.py install --prefix=$install_dir --install-scripts=$install_dir/bin --install-lib=$install_dir/lib/python2.7/site-packages >>$INSTALL_DIR/INSTALLATION.log 2>&1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	33 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	34 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	35 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	36 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	37 }
4 013bf1e2cc8f Updated to Amplicon_Analysis_pipeline v1.2.2. pjbriggs parents: 3 diff changeset	38 function install_amplicon_analysis_pipeline_1_2_2() {
013bf1e2cc8f Updated to Amplicon_Analysis_pipeline v1.2.2. pjbriggs parents: 3 diff changeset	39 install_amplicon_analysis_pipeline $1 1.2.2
013bf1e2cc8f Updated to Amplicon_Analysis_pipeline v1.2.2. pjbriggs parents: 3 diff changeset	40 }
2 a898ee628343 Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	41 function install_amplicon_analysis_pipeline_1_2_1() {
a898ee628343 Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	42 install_amplicon_analysis_pipeline $1 1.2.1
a898ee628343 Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	43 }
0 b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	44 function install_amplicon_analysis_pipeline_1_1() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	45 install_amplicon_analysis_pipeline $1 1.1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	46 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	47 function install_amplicon_analysis_pipeline_1_0() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	48 install_amplicon_analysis_pipeline $1 1.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	49 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	50 function install_amplicon_analysis_pipeline() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	51 version=$2
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	52 echo Installing Amplicon_analysis $version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	53 install_dir=$1/amplicon_analysis_pipeline/$version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	54 if [ -f $install_dir/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	55 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	56 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	57 mkdir -p $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	58 echo Moving to $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	59 pushd $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	60 wget -q https://github.com/MTutino/Amplicon_analysis/archive/v${version}.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	61 tar zxf v${version}.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	62 mv Amplicon_analysis-${version} Amplicon_analysis
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	63 rm -rf v${version}.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	64 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	65 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	66 cat > $install_dir/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	67 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	68 # Source this to setup Amplicon_analysis/$version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	69 echo Setting up Amplicon analysis pipeline $version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	70 export PATH=$install_dir/Amplicon_analysis:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	71 ## AMPLICON_ANALYSIS_REF_DATA_PATH should be set in
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	72 ## config/local_env.sh or in the job_conf.xml file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	73 ## - see the README
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	74 ##export AMPLICON_ANALYSIS_REF_DATA_PATH=
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	75 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	76 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	77 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	78 function install_amplicon_analysis_pipeline_1_0_patched() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	79 version="1.0-patched"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	80 echo Installing Amplicon_analysis $version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	81 install_dir=$1/amplicon_analysis_pipeline/$version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	82 if [ -f $install_dir/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	83 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	84 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	85 mkdir -p $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	86 echo Moving to $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	87 pushd $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	88 # Clone and patch analysis pipeline scripts
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	89 git clone https://github.com/pjbriggs/Amplicon_analysis.git
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	90 cd Amplicon_analysis
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	91 git checkout -b $version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	92 branches=
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	93 if [ ! -z "$branches" ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	94 for branch in $branches ; do
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	95 git checkout -b $branch origin/$branch
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	96 git checkout $version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	97 git merge -m "Merge $branch into $version" $branch
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	98 done
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	99 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	100 cd ..
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	101 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	102 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	103 cat > $install_dir/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	104 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	105 # Source this to setup Amplicon_analysis/$version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	106 echo Setting up Amplicon analysis pipeline $version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	107 export PATH=$install_dir/Amplicon_analysis:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	108 ## AMPLICON_ANALYSIS_REF_DATA_PATH should be set in
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	109 ## config/local_env.sh or in the job_conf.xml file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	110 ## - see the README
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	111 ##export AMPLICON_ANALYSIS_REF_DATA_PATH=
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	112 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	113 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	114 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	115 function install_cutadapt_1_11() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	116 echo Installing cutadapt 1.11
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	117 INSTALL_DIR=$1/cutadapt/1.11
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	118 if [ -f $INSTALL_DIR/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	119 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	120 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	121 mkdir -p $INSTALL_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	122 install_python_package $INSTALL_DIR cutadapt 1.11 \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	123 https://pypi.python.org/packages/47/bf/9045e90dac084a90aa2bb72c7d5aadefaea96a5776f445f5b5d9a7a2c78b/cutadapt-1.11.tar.gz \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	124 cutadapt-1.11
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	125 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	126 cat > $INSTALL_DIR/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	127 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	128 # Source this to setup cutadapt/1.11
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	129 echo Setting up cutadapt 1.11
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	130 #if [ -f $1/python/2.7.10/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	131 # . $1/python/2.7.10/env.sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	132 #fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	133 export PATH=$INSTALL_DIR/bin:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	134 export PYTHONPATH=$INSTALL_DIR:\$PYTHONPATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	135 export PYTHONPATH=$INSTALL_DIR/lib:\$PYTHONPATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	136 export PYTHONPATH=$INSTALL_DIR/lib/python2.7:\$PYTHONPATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	137 export PYTHONPATH=$INSTALL_DIR/lib/python2.7/site-packages:\$PYTHONPATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	138 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	139 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	140 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	141 function install_sickle_1_33() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	142 echo Installing sickle 1.33
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	143 INSTALL_DIR=$1/sickle/1.33
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	144 if [ -f $INSTALL_DIR/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	145 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	146 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	147 mkdir -p $INSTALL_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	148 mkdir -p $INSTALL_DIR/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	149 wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	150 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	151 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	152 wget -q https://github.com/najoshi/sickle/archive/v1.33.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	153 tar zxf v1.33.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	154 cd sickle-1.33
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	155 make >$INSTALL_DIR/INSTALLATION.log 2>&1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	156 mv sickle $INSTALL_DIR/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	157 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	158 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	159 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	160 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	161 cat > $INSTALL_DIR/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	162 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	163 # Source this to setup sickle/1.33
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	164 echo Setting up sickle 1.33
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	165 export PATH=$INSTALL_DIR/bin:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	166 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	167 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	168 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	169 function install_bioawk_27_08_2013() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	170 echo Installing bioawk 27-08-2013
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	171 INSTALL_DIR=$1/bioawk/27-08-2013
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	172 if [ -f $INSTALL_DIR/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	173 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	174 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	175 mkdir -p $INSTALL_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	176 mkdir -p $INSTALL_DIR/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	177 wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	178 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	179 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	180 wget -q https://github.com/lh3/bioawk/archive/v1.0.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	181 tar zxf v1.0.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	182 cd bioawk-1.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	183 make >$INSTALL_DIR/INSTALLATION.log 2>&1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	184 mv bioawk $INSTALL_DIR/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	185 mv maketab $INSTALL_DIR/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	186 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	187 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	188 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	189 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	190 cat > $INSTALL_DIR/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	191 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	192 # Source this to setup bioawk/2013-07-13
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	193 echo Setting up bioawk 2013-07-13
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	194 export PATH=$INSTALL_DIR/bin:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	195 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	196 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	197 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	198 function install_pandaseq_2_8_1() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	199 # Taken from https://github.com/fls-bioinformatics-core/galaxy-tools/blob/master/local_dependency_installers/pandaseq.sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	200 echo Installing pandaseq 2.8.1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	201 local install_dir=$1/pandaseq/2.8.1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	202 if [ -f $install_dir/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	203 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	204 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	205 mkdir -p $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	206 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	207 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	208 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	209 wget -q https://github.com/neufeld/pandaseq/archive/v2.8.1.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	210 tar xzf v2.8.1.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	211 cd pandaseq-2.8.1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	212 ./autogen.sh >$install_dir/INSTALLATION.log 2>&1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	213 ./configure --prefix=$install_dir >>$install_dir/INSTALLATION.log 2>&1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	214 make; make install >>$install_dir/INSTALLATION.log 2>&1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	215 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	216 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	217 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	218 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	219 cat > $1/pandaseq/2.8.1/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	220 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	221 # Source this to setup pandaseq/2.8.1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	222 echo Setting up pandaseq 2.8.1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	223 export PATH=$install_dir/bin:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	224 export LD_LIBRARY_PATH=$install_dir/lib:\$LD_LIBRARY_PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	225 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	226 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	227 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	228 function install_spades_3_5_0() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	229 # See http://spades.bioinf.spbau.ru/release3.5.0/manual.html
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	230 echo Installing spades 3.5.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	231 local install_dir=$1/spades/3.5.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	232 if [ -f $install_dir/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	233 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	234 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	235 mkdir -p $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	236 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	237 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	238 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	239 wget -q http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0-Linux.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	240 tar zxf SPAdes-3.5.0-Linux.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	241 cd SPAdes-3.5.0-Linux
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	242 mv bin $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	243 mv share $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	244 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	245 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	246 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	247 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	248 cat > $1/spades/3.5.0/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	249 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	250 # Source this to setup spades/3.5.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	251 echo Setting up spades 3.5.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	252 export PATH=$install_dir/bin:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	253 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	254 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	255 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	256 function install_fastqc_0_11_3() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	257 echo Installing fastqc 0.11.3
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	258 local install_dir=$1/fastqc/0.11.3
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	259 if [ -f $install_dir/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	260 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	261 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	262 mkdir -p $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	263 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	264 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	265 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	266 wget -q http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.3.zip
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	267 unzip -qq fastqc_v0.11.3.zip
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	268 cd FastQC
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	269 chmod 0755 fastqc
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	270 mv * $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	271 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	272 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	273 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	274 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	275 cat > $1/fastqc/0.11.3/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	276 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	277 # Source this to setup fastqc/0.11.3
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	278 echo Setting up fastqc 0.11.3
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	279 export PATH=$install_dir:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	280 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	281 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	282 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	283 function install_qiime_1_8_0() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	284 # See http://qiime.org/1.8.0/install/install.html
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	285 echo Installing qiime 1.8.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	286 INSTALL_DIR=$1/qiime/1.8.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	287 if [ -f $INSTALL_DIR/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	288 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	289 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	290 mkdir -p $INSTALL_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	291 # Atlas 3.10 (precompiled)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	292 # NB this stolen from galaxyproject/iuc-tools
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	293 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	294 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	295 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	296 wget -q https://depot.galaxyproject.org/software/atlas/atlas_3.10.2_linux_x64.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	297 tar zxvf atlas_3.10.2_linux_x64.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	298 mv lib $INSTALL_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	299 command -v gfortran \|\| return 0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	300 BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	301 BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON \| grep GFORTRAN_1 \| sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' \| sort -n \| tail -1`
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	302 echo 'program test; end program test' > test.f90
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	303 gfortran -o test test.f90
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	304 LGF=`ldd test \| grep libgfortran \| awk '{print $3}'`
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	305 LGF_CANON=`readlink -f $LGF`
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	306 LGF_VERS=`objdump -p $LGF_CANON \| grep GFORTRAN_1 \| sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' \| sort -n \| tail -1`
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	307 if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	308 cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	309 cp -p $LGF_CANON $BUNDLED_LGF_CANON
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	310 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	311 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	312 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	313 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	314 # Atlas 3.10 (build from source)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	315 # NB this stolen from galaxyproject/iuc-tools
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	316 ##local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	317 ##echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	318 ##pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	319 ##wget -q https://depot.galaxyproject.org/software/atlas/atlas_3.10.2+gx0_src_all.tar.bz2
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	320 ##wget -q https://depot.galaxyproject.org/software/lapack/lapack_3.5.0_src_all.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	321 ##wget -q https://depot.galaxyproject.org/software/atlas/atlas_patch-blas-lapack-1.0_src_all.diff
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	322 ##wget -q https://depot.galaxyproject.org/software/atlas/atlas_patch-shared-lib-1.0_src_all.diff
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	323 ##wget -q https://depot.galaxyproject.org/software/atlas/atlas_patch-cpu-throttle-1.0_src_all.diff
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	324 ##tar -jxvf atlas_3.10.2+gx0_src_all.tar.bz2
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	325 ##cd ATLAS
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	326 ##mkdir build
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	327 ##patch -p1 < ../atlas_patch-blas-lapack-1.0_src_all.diff
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	328 ##patch -p1 < ../atlas_patch-shared-lib-1.0_src_all.diff
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	329 ##patch -p1 < ../atlas_patch-cpu-throttle-1.0_src_all.diff
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	330 ##cd build
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	331 ##../configure --prefix="$INSTALL_DIR" -D c -DWALL -b 64 -Fa alg '-fPIC' --with-netlib-lapack-tarfile=../../lapack_3.5.0_src_all.tar.gz -v 2 -t 0 -Si cputhrchk 0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	332 ##make
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	333 ##make install
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	334 ##popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	335 ##rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	336 ##rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	337 export ATLAS_LIB_DIR=$INSTALL_DIR/lib
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	338 export ATLAS_INCLUDE_DIR=$INSTALL_DIR/include
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	339 export ATLAS_BLAS_LIB_DIR=$INSTALL_DIR/lib/atlas
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	340 export ATLAS_LAPACK_LIB_DIR=$INSTALL_DIR/lib/atlas
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	341 export ATLAS_ROOT_PATH=$INSTALL_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	342 export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	343 export LD_LIBRARY_PATH=$INSTALL_DIR/lib/atlas:$LD_LIBRARY_PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	344 # Numpy 1.7.1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	345 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	346 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	347 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	348 wget -q https://depot.galaxyproject.org/software/numpy/numpy_1.7_src_all.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	349 tar -zxvf numpy_1.7_src_all.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	350 cd numpy-1.7.1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	351 cat > site.cfg <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	352 [DEFAULT]
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	353 library_dirs = $ATLAS_LIB_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	354 include_dirs = $ATLAS_INCLUDE_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	355 [blas_opt]
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	356 libraries = blas, atlas
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	357 [lapack_opt]
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	358 libraries = lapack, atlas
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	359 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	360 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python2.7
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	361 export ATLAS=$ATLAS_ROOT_PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	362 python setup.py install --install-lib $INSTALL_DIR/lib/python2.7 --install-scripts $INSTALL_DIR/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	363 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	364 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	365 rmdir $wd
3 b9e2b3dd392d Removed unwanted changes to install_tool_deps.sh in previous upload. pjbriggs parents: 2 diff changeset	366 # Python packages
b9e2b3dd392d Removed unwanted changes to install_tool_deps.sh in previous upload. pjbriggs parents: 2 diff changeset	367 ##install_python_package $INSTALL_DIR numpy 1.7.1 \
b9e2b3dd392d Removed unwanted changes to install_tool_deps.sh in previous upload. pjbriggs parents: 2 diff changeset	368 ## https://pypi.python.org/packages/84/fb/5e9dfeeb5d8909d659e6892c97c9aa66d3798fad50e1d3d66b3c614a9c35/numpy-1.7.1.tar.gz \
b9e2b3dd392d Removed unwanted changes to install_tool_deps.sh in previous upload. pjbriggs parents: 2 diff changeset	369 ## numpy-1.7.1
b9e2b3dd392d Removed unwanted changes to install_tool_deps.sh in previous upload. pjbriggs parents: 2 diff changeset	370 install_python_package $INSTALL_DIR matplotlib 1.3.1 \
b9e2b3dd392d Removed unwanted changes to install_tool_deps.sh in previous upload. pjbriggs parents: 2 diff changeset	371 https://pypi.python.org/packages/d4/d0/17f17792a4d50994397052220dbe3ac9850ecbde0297b7572933fa4a5c98/matplotlib-1.3.1.tar.gz \
b9e2b3dd392d Removed unwanted changes to install_tool_deps.sh in previous upload. pjbriggs parents: 2 diff changeset	372 matplotlib-1.3.1
0 b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	373 install_python_package $INSTALL_DIR qiime 1.8.0 \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	374 https://github.com/biocore/qiime/archive/1.8.0.tar.gz \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	375 qiime-1.8.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	376 install_python_package $INSTALL_DIR pycogent 1.5.3 \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	377 https://pypi.python.org/packages/1f/9f/c6f6afe09a3d62a6e809c7745413ffff0f1e8e04d88ab7b56faedf31fe28/cogent-1.5.3.tgz \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	378 cogent-1.5.3
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	379 install_python_package $INSTALL_DIR pyqi 0.3.1 \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	380 https://pypi.python.org/packages/60/f0/a7392f5f5caf59a50ccaddbb35a458514953512b7dd6053567cb02849c6e/pyqi-0.3.1.tar.gz \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	381 pyqi-0.3.1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	382 install_python_package $INSTALL_DIR biom-format 1.3.1 \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	383 https://pypi.python.org/packages/98/3b/4e80a9a5c4a3c6764aa8c0c994973e7df71eee02fc6b8cc6e1d06a64ab7e/biom-format-1.3.1.tar.gz \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	384 biom-format-1.3.1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	385 install_python_package $INSTALL_DIR qcli 0.1.0 \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	386 https://pypi.python.org/packages/9a/9a/9c634aed339a5f063e0c954ae439d03b33a7159aa50c6f21034fe2d48fe8/qcli-0.1.0.tar.gz \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	387 qcli-0.1.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	388 install_python_package $INSTALL_DIR pynast 1.2.2 \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	389 https://pypi.python.org/packages/a0/82/f381ff91afd7a2d92e74c7790823e256d87d5cd0a98c12eaac3d3ec64b8f/pynast-1.2.2.tar.gz \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	390 pynast-1.2.2
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	391 install_python_package $INSTALL_DIR emperor 0.9.3 \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	392 https://pypi.python.org/packages/cd/f1/5d502a16a348efe1af7a8d4f41b639c9a165bca0b2f9db36bce89ad1ab40/emperor-0.9.3.tar.gz \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	393 emperor-0.9.3
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	394 # Update the acceptable Python version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	395 sed -i 's/acceptable_version = (2,7,3)/acceptable_version = (2,7,6)/g' $INSTALL_DIR/bin/print_qiime_config.py
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	396 # Non-Python dependencies
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	397 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	398 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	399 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	400 wget -q http://www.microbesonline.org/fasttree/FastTree
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	401 chmod 0755 FastTree
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	402 mv FastTree $INSTALL_DIR/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	403 # Config file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	404 sed -i 's,qiime_scripts_dir,qiime_scripts_dir\t'"$INSTALL_DIR\/bin"',g' $INSTALL_DIR/lib/python2.7/site-packages/qiime/support_files/qiime_config
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	405 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	406 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	407 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	408 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	409 cat > $INSTALL_DIR/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	410 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	411 # Source this to setup qiime/1.8.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	412 echo Setting up qiime 1.8.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	413 #if [ -f $1/python/2.7.10/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	414 # . $1/python/2.7.10/env.sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	415 #fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	416 export QIIME_CONFIG_FP=$INSTALL_DIR/lib/python2.7/site-packages/qiime/support_files/qiime_config
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	417 export PATH=$INSTALL_DIR/bin:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	418 export PYTHONPATH=$INSTALL_DIR:\$PYTHONPATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	419 export PYTHONPATH=$INSTALL_DIR/lib:\$PYTHONPATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	420 export PYTHONPATH=$INSTALL_DIR/lib/python2.7:\$PYTHONPATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	421 export PYTHONPATH=$INSTALL_DIR/lib/python2.7/site-packages:\$PYTHONPATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	422 export LD_LIBRARY_PATH=$ATLAS_LIB_DIR:\$LD_LIBRARY_PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	423 export LD_LIBRARY_PATH=$ATLAS_LIB_DIR/atlas::\$LD_LIBRARY_PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	424 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	425 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	426 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	427 function install_vsearch_1_1_3() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	428 echo Installing vsearch 1.1.3
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	429 local install_dir=$1/vsearch/1.1.3
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	430 if [ -f $install_dir/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	431 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	432 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	433 mkdir -p $install_dir/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	434 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	435 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	436 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	437 wget -q https://github.com/torognes/vsearch/releases/download/v1.1.3/vsearch-1.1.3-linux-x86_64
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	438 chmod 0755 vsearch-1.1.3-linux-x86_64
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	439 mv vsearch-1.1.3-linux-x86_64 $install_dir/bin/vsearch
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	440 ln -s $install_dir/bin/vsearch $install_dir/bin/vsearch113
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	441 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	442 # Clean up
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	443 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	444 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	445 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	446 cat > $install_dir/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	447 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	448 # Source this to setup vsearch/1.1.3
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	449 echo Setting up vsearch 1.1.3
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	450 export PATH=$install_dir/bin:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	451 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	452 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	453 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	454 function install_microbiomeutil_2010_04_29() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	455 # Provides ChimeraSlayer
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	456 echo Installing microbiomeutil 2010-04-29
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	457 local install_dir=$1/microbiomeutil/2010-04-29
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	458 if [ -f $install_dir/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	459 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	460 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	461 mkdir -p $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	462 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	463 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	464 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	465 wget -q https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	466 tar zxf microbiomeutil_2010-04-29.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	467 cd microbiomeutil_2010-04-29
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	468 make >$install_dir/INSTALLATION.log 2>&1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	469 mv * $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	470 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	471 # Clean up
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	472 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	473 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	474 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	475 cat > $install_dir/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	476 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	477 # Source this to setup microbiomeutil/2010-04-29
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	478 echo Setting up microbiomeutil 2010-04-29
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	479 export PATH=$install_dir/ChimeraSlayer:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	480 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	481 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	482 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	483 function install_blast_2_2_26() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	484 echo Installing blast 2.2.26
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	485 local install_dir=$1/blast/2.2.26
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	486 if [ -f $install_dir/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	487 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	488 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	489 mkdir -p $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	490 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	491 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	492 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	493 wget -q ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/blast-2.2.26-x64-linux.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	494 tar zxf blast-2.2.26-x64-linux.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	495 cd blast-2.2.26
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	496 mv * $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	497 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	498 # Clean up
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	499 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	500 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	501 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	502 cat > $install_dir/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	503 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	504 # Source this to setup blast/2.2.26
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	505 echo Setting up blast 2.2.26
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	506 export PATH=$install_dir/bin:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	507 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	508 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	509 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	510 function install_fasta_number() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	511 # See http://drive5.com/python/fasta_number_py.html
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	512 echo Installing fasta_number
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	513 # Install to "default" version i.e. essentially a versionless
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	514 # installation (see Galaxy dependency resolver docs)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	515 local install_dir=$1/fasta_number
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	516 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	517 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	518 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	519 # Download and use MD5 as local version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	520 wget -q http://drive5.com/python/python_scripts.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	521 local version=$(md5sum python_scripts.tar.gz \| cut -d" " -f1)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	522 # Check for existing installation
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	523 local default_dir=$install_dir/default
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	524 install_dir=$install_dir/$version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	525 if [ -f $install_dir/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	526 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	527 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	528 # Install scripts and make 'default' link
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	529 mkdir -p $install_dir/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	530 mkdir -p $install_dir/lib
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	531 tar zxf python_scripts.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	532 mv fasta_number.py $install_dir/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	533 mv die.py $install_dir/lib
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	534 ln -s $version $default_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	535 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	536 # Clean up
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	537 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	538 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	539 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	540 cat > $install_dir/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	541 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	542 # Source this to setup fasta_number/$version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	543 echo Setting up fasta_number $version
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	544 export PATH=$install_dir/bin:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	545 export PYTHONPATH=$install_dir/lib:\$PYTHONPATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	546 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	547 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	548 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	549 function install_fasta_splitter_0_2_4() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	550 echo Installing fasta-splitter 0.2.4
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	551 local install_dir=$1/fasta-splitter/0.2.4
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	552 if [ -f $install_dir/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	553 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	554 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	555 mkdir -p $install_dir/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	556 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	557 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	558 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	559 # Install Perl packages using cpanm
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	560 mkdir -p $install_dir/lib/perl5
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	561 wget -q -L https://cpanmin.us/ -O cpanm
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	562 chmod +x cpanm
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	563 for package in "File::Util" ; do
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	564 /bin/bash <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	565 export PATH=$install_dir/bin:$PATH PERL5LIB=$install_dir/lib/perl5:$PERL5LIB && \
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	566 ./cpanm -l $install_dir $package >>$install_dir/INSTALLATION.log
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	567 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	568 done
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	569 # Install fasta-splitter
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	570 wget -q http://kirill-kryukov.com/study/tools/fasta-splitter/files/fasta-splitter-0.2.4.zip
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	571 unzip -qq fasta-splitter-0.2.4.zip
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	572 chmod 0755 fasta-splitter.pl
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	573 mv fasta-splitter.pl $install_dir/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	574 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	575 # Clean up
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	576 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	577 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	578 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	579 cat > $install_dir/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	580 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	581 # Source this to setup fasta-splitter/0.2.4
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	582 echo Setting up fasta-splitter 0.2.4
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	583 export PATH=$install_dir/bin:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	584 export PERL5LIB=$install_dir/lib/perl5:\$PERL5LIB
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	585 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	586 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	587 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	588 function install_rdp_classifier_2_2() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	589 echo Installing rdp-classifier 2.2R
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	590 local install_dir=$1/rdp-classifier/2.2
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	591 if [ -f $install_dir/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	592 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	593 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	594 mkdir -p $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	595 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	596 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	597 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	598 wget -q https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.2.zip
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	599 unzip -qq rdp_classifier_2.2.zip
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	600 cd rdp_classifier_2.2
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	601 mv * $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	602 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	603 # Clean up
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	604 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	605 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	606 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	607 cat > $install_dir/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	608 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	609 # Source this to setup rdp-classifier/2.2
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	610 echo Setting up RDP classifier 2.2
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	611 export RDP_JAR_PATH=$install_dir/rdp_classifier-2.2.jar
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	612 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	613 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	614 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	615 function install_R_3_2_0() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	616 # Adapted from https://github.com/fls-bioinformatics-core/galaxy-tools/blob/master/local_dependency_installers/R.sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	617 echo Installing R 3.2.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	618 local install_dir=$1/R/3.2.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	619 if [ -f $install_dir/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	620 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	621 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	622 mkdir -p $install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	623 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	624 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	625 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	626 wget -q http://cran.r-project.org/src/base/R-3/R-3.2.0.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	627 tar xzf R-3.2.0.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	628 cd R-3.2.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	629 ./configure --prefix=$install_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	630 make
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	631 make install
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	632 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	633 # Clean up
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	634 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	635 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	636 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	637 cat > $install_dir/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	638 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	639 # Source this to setup R/3.2.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	640 echo Setting up R 3.2.0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	641 export PATH=$install_dir/bin:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	642 export TCL_LIBRARY=$install_dir/lib/libtcl8.4.so
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	643 export TK_LIBRARY=$install_dir/lib/libtk8.4.so
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	644 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	645 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	646 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	647 function install_uc2otutab() {
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	648 # See http://drive5.com/python/uc2otutab_py.html
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	649 echo Installing uc2otutab
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	650 # Install to "default" version i.e. essentially a versionless
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	651 # installation (see Galaxy dependency resolver docs)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	652 local install_dir=$1/uc2otutab/default
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	653 if [ -f $install_dir/env.sh ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	654 return
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	655 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	656 mkdir -p $install_dir/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	657 local wd=$(mktemp -d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	658 echo Moving to $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	659 pushd $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	660 wget -q http://drive5.com/python/python_scripts.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	661 tar zxf python_scripts.tar.gz
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	662 mv die.py fasta.py progress.py uc.py $install_dir/bin
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	663 echo "#!/usr/bin/env python" >$install_dir/bin/uc2otutab.py
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	664 cat uc2otutab.py >>$install_dir/bin/uc2otutab.py
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	665 chmod +x $install_dir/bin/uc2otutab.py
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	666 popd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	667 # Clean up
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	668 rm -rf $wd/*
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	669 rmdir $wd
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	670 # Make setup file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	671 cat > $install_dir/env.sh <<EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	672 #!/bin/sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	673 # Source this to setup uc2otutab/default
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	674 echo Setting up uc2otutab $default$
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	675 export PATH=$install_dir/bin:\$PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	676 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	677 EOF
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	678 }
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	679 ##########################################################
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	680 # Main script starts here
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	681 ##########################################################
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	682 # Fetch top-level installation directory from command line
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	683 TOP_DIR=$1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	684 if [ -z "$TOP_DIR" ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	685 echo Usage: $(basename $0) DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	686 exit
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	687 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	688 if [ -z "$(echo $TOP_DIR \| grep ^/)" ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	689 TOP_DIR=$(pwd)/$TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	690 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	691 if [ ! -d "$TOP_DIR" ] ; then
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	692 mkdir -p $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	693 fi
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	694 # Install dependencies
4 013bf1e2cc8f Updated to Amplicon_Analysis_pipeline v1.2.2. pjbriggs parents: 3 diff changeset	695 install_amplicon_analysis_pipeline_1_2_2 $TOP_DIR
0 b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	696 install_cutadapt_1_11 $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	697 install_sickle_1_33 $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	698 install_bioawk_27_08_2013 $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	699 install_pandaseq_2_8_1 $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	700 install_spades_3_5_0 $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	701 install_fastqc_0_11_3 $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	702 install_qiime_1_8_0 $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	703 install_vsearch_1_1_3 $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	704 install_microbiomeutil_2010_04_29 $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	705 install_blast_2_2_26 $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	706 install_fasta_number $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	707 install_fasta_splitter_0_2_4 $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	708 install_rdp_classifier_2_2 $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	709 install_R_3_2_0 $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	710 install_uc2otutab $TOP_DIR
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	711 ##
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	712 #

Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate install_tool_deps.sh @ 37:e832be1635b4 draft