diff env/envbootstrap.sh @ 0:d67268158946 draft

planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/envbootstrap.sh	Mon Oct 12 17:43:33 2015 -0400
@@ -0,0 +1,120 @@
+#!/bin/bash
+# Usage: envbootstrap.sh [Options]
+
+# Create a virtualenv, and install requirements to it.
+
+# Requirements: wget, tar, git
+
+
+#set -e
+
+
+# Vars/options
+SCRIPT_LOCATION=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)
+VENV_VERSION=1.11.6
+
+# options configurable from the command line
+VENV=$(basename $(cd $SCRIPT_LOCATION/.. && pwd))-env
+PYTHON=$(which python)
+PY_VERSION=$($PYTHON -c 'import sys; print "{}.{}.{}".format(*sys.version_info[:3])')
+REQFILE=$SCRIPT_LOCATION/requirements.txt
+
+if [[ $1 == '-h' || $1 == '--help' ]]; then
+    echo "Create a virtualenv and install all pipeline dependencies"
+    echo "Options:"
+    echo "--venv            - path of virtualenv [$VENV]"
+    echo "--python          - path to an alternative python interpreter [$PYTHON]"
+    echo "--requirements    - an alternative requiremets file [$REQFILE]"
+    exit 0
+fi
+
+while true; do
+    case "$1" in
+  --venv ) VENV="$2"; shift 2 ;;
+  --python ) PYTHON="$2"; shift 2 ;;
+  --requirements ) REQFILE="$2"; shift 2 ;;
+  * ) break ;;
+    esac
+done
+
+mkdir -p src
+
+# Create the virtualenv using a specified version of the virtualenv
+# source. This also provides setuptools and pip. Inspired by
+# http://eli.thegreenplace.net/2013/04/20/bootstrapping-virtualenv/
+
+# create virtualenv if necessary
+if [ ! -f ${VENV:?}/bin/activate ]; then
+    # download virtualenv source if necessary
+    if [ ! -f src/virtualenv-${VENV_VERSION}/virtualenv.py ]; then
+       VENV_URL='https://pypi.python.org/packages/source/v/virtualenv'
+       (cd src && \
+          wget -N ${VENV_URL}/virtualenv-${VENV_VERSION}.tar.gz && \
+          tar -xf virtualenv-${VENV_VERSION}.tar.gz)
+    fi
+    $PYTHON src/virtualenv-${VENV_VERSION}/virtualenv.py $VENV
+    $PYTHON src/virtualenv-${VENV_VERSION}/virtualenv.py --relocatable $VENV
+else
+    echo "found existing virtualenv $VENV"
+fi
+
+# Activate our new (or existing) virtual env
+source $VENV/bin/activate
+# contains the absolute path
+VENV=$VIRTUAL_ENV
+
+# Start an env.sh file
+echo ". $VENV/bin/activate" > $VENV/env.sh
+
+venv_abspath=$(readlink -f $VENV)
+
+# First install all python requirements
+pip install numpy
+pip install scipy
+pip install biopython
+pip install lxml
+pip install -r $REQFILE
+
+# Next install R requirements, and set up R_LIBS export in env.sh
+R_LIBS=$VENV/lib/R
+mkdir -p $R_LIBS
+R_LIBS=$R_LIBS $SCRIPT_LOCATION/rdeps.R
+
+echo "R_LIBS=$R_LIBS ; export R_LIBS" >> $VENV/env.sh
+
+
+# For everything else, we'll try to use encapish setup
+ENCAP=$VENV/encap
+mkdir -p $ENCAP
+
+
+# Next install BEAST
+if [[ ! -f $VENV/bin/beast ]]; then
+  (cd $ENCAP && \
+    rm -rf BEAST.v2.1.3.tgz BEAST && \
+    wget -N https://github.com/CompEvol/beast2/releases/download/v2.1.3/BEAST.v2.1.3.tgz && \
+    tar -zxf BEAST.v2.1.3.tgz && \
+    (ln -s ../encap/BEAST/bin/* ../bin/ & \
+      ln -s ../encap/BEAST/lib/* ../lib))
+fi
+
+# Add the BEAST_CLASSIC package
+addonmanager -add BEASTlabs
+addonmanager -add BEAST_CLASSIC
+
+
+# Next install PACT
+if [[ ! -f $VENV/bin/pact ]]; then
+  (cd $ENCAP && \
+    rm -rf PACT && \
+    git clone https://github.com/trvrb/PACT.git && \
+    cd PACT && \
+    make && \
+    cd .. && \
+    ln -s ../encap/PACT/pact ../bin/pact
+    )
+fi
+
+# correct any more shebang lines
+virtualenv --relocatable $VENV
+