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annotate install_tool_deps.sh @ 3:f8a9a5eaca8a draft

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Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
author pjbriggs
date Wed, 23 Sep 2015 08:59:23 -0400
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1 #!/bin/bash
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2 #
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3 # Install dependencies for Trimmomatic for testing from the command line
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4 #
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5 # Installation directory
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6 TOP_DIR=$1
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7 if [ -z "$TOP_DIR" ] ; then
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8 echo Usage: $(basename $0) DIR
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9 exit
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10 fi
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11 if [ -z "$(echo $TOP_DIR | grep ^/)" ] ; then
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12 TOP_DIR=$(pwd)/$TOP_DIR
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13 fi
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14 if [ ! -d "$TOP_DIR" ] ; then
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15 mkdir -p $TOP_DIR
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16 fi
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17 cd $TOP_DIR
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18 # Trimmomatic 0.32
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19 INSTALL_DIR=$TOP_DIR/trimmomatic/0.32
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20 mkdir -p $INSTALL_DIR
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21 wd=$(mktemp -d)
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22 pushd $wd
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23 wget -q http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
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24 unzip -qq Trimmomatic-0.32.zip
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25 mv Trimmomatic-0.32/trimmomatic-0.32.jar $INSTALL_DIR/
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26 mv Trimmomatic-0.32/adapters/ $INSTALL_DIR/
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27 popd
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28 rm -rf $wd/*
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29 rmdir $wd
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30 # Make setup file
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31 cat > trimmomatic/0.32/env.sh <<EOF
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32 #!/bin/sh
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33 # Source this to setup trimmomatic/0.32
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34 echo Setting up Trimmomatic 0.32
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35 export TRIMMOMATIC_DIR=$INSTALL_DIR
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36 export TRIMMOMATIC_ADAPTERS_DIR=$INSTALL_DIR/adapters
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37 #
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38 EOF
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39 ##
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40 #