diff install_tool_deps.sh @ 2:a898ee628343 draft

Updated to version 1.2.1.0

--- a/install_tool_deps.sh	Thu Nov 09 10:09:33 2017 -0500
+++ b/install_tool_deps.sh	Wed Apr 25 03:45:37 2018 -0400
@@ -35,6 +35,9 @@
     rm -rf $wd/*
     rmdir $wd
 }
+function install_amplicon_analysis_pipeline_1_2_1() {
+    install_amplicon_analysis_pipeline $1 1.2.1
+}
 function install_amplicon_analysis_pipeline_1_1() {
     install_amplicon_analysis_pipeline $1 1.1
 }
@@ -335,6 +338,9 @@
     export ATLAS_ROOT_PATH=$INSTALL_DIR
     export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH
     export LD_LIBRARY_PATH=$INSTALL_DIR/lib/atlas:$LD_LIBRARY_PATH
+    # Make installation directories
+    mkdir -p $INSTALL_DIR/bin
+    mkdir -p $INSTALL_DIR/lib/python2.7/site-packages
     # Numpy 1.7.1
     local wd=$(mktemp -d)
     echo Moving to $wd
@@ -357,13 +363,49 @@
     popd
     rm -rf $wd/*
     rmdir $wd
-    # Python packages
-    ##install_python_package $INSTALL_DIR numpy 1.7.1 \
-    ## https://pypi.python.org/packages/84/fb/5e9dfeeb5d8909d659e6892c97c9aa66d3798fad50e1d3d66b3c614a9c35/numpy-1.7.1.tar.gz \
-    ## numpy-1.7.1
-    install_python_package $INSTALL_DIR matplotlib 1.3.1 \
-	https://pypi.python.org/packages/d4/d0/17f17792a4d50994397052220dbe3ac9850ecbde0297b7572933fa4a5c98/matplotlib-1.3.1.tar.gz \
-	matplotlib-1.3.1
+    # Setuptools 36.4.0
+    install_python_package $INSTALL_DIR setuptools 38.2.4 \
+	https://github.com/pypa/setuptools/archive/v38.2.4.tar.gz \
+	setuptools-38.2.4
+    # Distribute 0.6.28
+    ##local wd=$(mktemp -d)
+    ##echo Moving to $wd
+    ##pushd $wd
+    ##wget -q https://pypi.python.org/packages/source/d/distribute/distribute-0.6.28.tar.gz
+    ##tar -zxvf distribute-0.6.28.tar.gz
+    ##cd distribute-0.6.28
+    ##sed -i 's,index_url="http://pypi.python.org/simple",index_url="https://pypi.python.org/simple",g' setuptools/package_index.py
+    ##sed -i 's,"http://pypi.python.org/simple","https://pypi.python.org/simple",g' setuptools/command/easy_install.py
+    ##/bin/bash <<EOF
+##export PYTHONPATH=$INSTALL_DIR:$PYTHONPATH && \
+##export PYTHONPATH=$INSTALL_DIR/lib/python2.7/site-packages:$PYTHONPATH && \
+##python setup.py install --prefix=$INSTALL_DIR --install-scripts=$INSTALL_DIR/bin --install-lib=$INSTALL_DIR/lib/python2.7/site-packages
+##EOF
+    ##python setup.py install --install-lib $INSTALL_DIR/lib/python2.7 --install-scripts $INSTALL_DIR/bin
+    ##popd
+    ##rm -rf $wd/*
+    ##rmdir $wd
+    # Matplotlib 1.3.1
+    local wd=$(mktemp -d)
+    echo Moving to $wd
+    pushd $wd
+    wget -q https://pypi.python.org/packages/d4/d0/17f17792a4d50994397052220dbe3ac9850ecbde0297b7572933fa4a5c98/matplotlib-1.3.1.tar.gz
+    tar -zxvf matplotlib-1.3.1.tar.gz
+    cd matplotlib-1.3.1
+    sed -i 's,http://pypi.python.org/packages/source/d/distribute/,https://pypi.python.org/packages/source/d/distribute/,g' distribute_setup.py
+    /bin/bash <<EOF
+export PYTHONPATH=$INSTALL_DIR:$PYTHONPATH && \
+export PYTHONPATH=$INSTALL_DIR/lib/python2.7/site-packages:$PYTHONPATH && \
+python setup.py install --prefix=$INSTALL_DIR --install-scripts=$INSTALL_DIR/bin --install-lib=$INSTALL_DIR/lib/python2.7/site-packages
+EOF
+    ##python setup.py install --install-lib $INSTALL_DIR/lib/python2.7 --install-scripts $INSTALL_DIR/bin
+    popd
+    rm -rf $wd/*
+    rmdir $wd
+    # Remaining Python packages
+    ##install_python_package $INSTALL_DIR matplotlib 1.3.1 \
+	##https://pypi.python.org/packages/d4/d0/17f17792a4d50994397052220dbe3ac9850ecbde0297b7572933fa4a5c98/matplotlib-1.3.1.tar.gz \
+	##matplotlib-1.3.1
     install_python_package $INSTALL_DIR qiime 1.8.0 \
 	https://github.com/biocore/qiime/archive/1.8.0.tar.gz \
 	qiime-1.8.0
@@ -686,7 +728,7 @@
     mkdir -p $TOP_DIR
 fi
 # Install dependencies
-install_amplicon_analysis_pipeline_1_1 $TOP_DIR
+install_amplicon_analysis_pipeline_1_2_1 $TOP_DIR
 install_cutadapt_1_11 $TOP_DIR
 install_sickle_1_33 $TOP_DIR
 install_bioawk_27_08_2013 $TOP_DIR