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author bcclaywell
date Mon, 12 Oct 2015 17:57:38 -0400
parents d67268158946
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1 #!/bin/bash
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2 # Usage: envbootstrap.sh [Options]
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3
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4 # Create a virtualenv, and install requirements to it.
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5
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6 # Requirements: wget, tar, git
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7
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8
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9 #set -e
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10
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11
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12 # Vars/options
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13 SCRIPT_LOCATION=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)
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14 VENV_VERSION=1.11.6
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15
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16 # options configurable from the command line
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17 VENV=$(basename $(cd $SCRIPT_LOCATION/.. && pwd))-env
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18 PYTHON=$(which python)
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19 PY_VERSION=$($PYTHON -c 'import sys; print "{}.{}.{}".format(*sys.version_info[:3])')
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20 REQFILE=$SCRIPT_LOCATION/requirements.txt
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21
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22 if [[ $1 == '-h' || $1 == '--help' ]]; then
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23 echo "Create a virtualenv and install all pipeline dependencies"
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24 echo "Options:"
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25 echo "--venv - path of virtualenv [$VENV]"
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26 echo "--python - path to an alternative python interpreter [$PYTHON]"
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27 echo "--requirements - an alternative requiremets file [$REQFILE]"
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28 exit 0
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29 fi
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30
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31 while true; do
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32 case "$1" in
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33 --venv ) VENV="$2"; shift 2 ;;
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34 --python ) PYTHON="$2"; shift 2 ;;
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35 --requirements ) REQFILE="$2"; shift 2 ;;
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36 * ) break ;;
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37 esac
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38 done
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39
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40 mkdir -p src
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41
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42 # Create the virtualenv using a specified version of the virtualenv
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43 # source. This also provides setuptools and pip. Inspired by
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44 # http://eli.thegreenplace.net/2013/04/20/bootstrapping-virtualenv/
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45
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46 # create virtualenv if necessary
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47 if [ ! -f ${VENV:?}/bin/activate ]; then
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48 # download virtualenv source if necessary
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49 if [ ! -f src/virtualenv-${VENV_VERSION}/virtualenv.py ]; then
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50 VENV_URL='https://pypi.python.org/packages/source/v/virtualenv'
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51 (cd src && \
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52 wget -N ${VENV_URL}/virtualenv-${VENV_VERSION}.tar.gz && \
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53 tar -xf virtualenv-${VENV_VERSION}.tar.gz)
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54 fi
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55 $PYTHON src/virtualenv-${VENV_VERSION}/virtualenv.py $VENV
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56 $PYTHON src/virtualenv-${VENV_VERSION}/virtualenv.py --relocatable $VENV
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57 else
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58 echo "found existing virtualenv $VENV"
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59 fi
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60
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61 # Activate our new (or existing) virtual env
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62 source $VENV/bin/activate
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63 # contains the absolute path
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64 VENV=$VIRTUAL_ENV
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65
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66 # Start an env.sh file
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67 echo ". $VENV/bin/activate" > $VENV/env.sh
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68
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69 venv_abspath=$(readlink -f $VENV)
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70
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71 # First install all python requirements
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72 pip install numpy
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73 pip install scipy
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74 pip install biopython
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75 pip install lxml
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76 pip install -r $REQFILE
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77
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78 # Next install R requirements, and set up R_LIBS export in env.sh
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79 R_LIBS=$VENV/lib/R
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80 mkdir -p $R_LIBS
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81 R_LIBS=$R_LIBS $SCRIPT_LOCATION/rdeps.R
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82
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83 echo "R_LIBS=$R_LIBS ; export R_LIBS" >> $VENV/env.sh
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84
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85
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86 # For everything else, we'll try to use encapish setup
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87 ENCAP=$VENV/encap
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88 mkdir -p $ENCAP
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89
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90
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91 # Next install BEAST
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92 if [[ ! -f $VENV/bin/beast ]]; then
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93 (cd $ENCAP && \
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94 rm -rf BEAST.v2.1.3.tgz BEAST && \
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95 wget -N https://github.com/CompEvol/beast2/releases/download/v2.1.3/BEAST.v2.1.3.tgz && \
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96 tar -zxf BEAST.v2.1.3.tgz && \
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97 (ln -s ../encap/BEAST/bin/* ../bin/ & \
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98 ln -s ../encap/BEAST/lib/* ../lib))
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99 fi
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100
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101 # Add the BEAST_CLASSIC package
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102 addonmanager -add BEASTlabs
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103 addonmanager -add BEAST_CLASSIC
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104
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105
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106 # Next install PACT
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107 if [[ ! -f $VENV/bin/pact ]]; then
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108 (cd $ENCAP && \
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109 rm -rf PACT && \
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110 git clone https://github.com/trvrb/PACT.git && \
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111 cd PACT && \
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112 make && \
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113 cd .. && \
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114 ln -s ../encap/PACT/pact ../bin/pact
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115 )
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116 fi
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117
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118 # correct any more shebang lines
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119 virtualenv --relocatable $VENV
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120