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comparison install_tool_deps.sh @ 3:a7139c612c45 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 08:48:20 -0400
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2:e7c8359dfa23 3:a7139c612c45
1 #!/bin/bash
2 #
3 # Install dependencies for Trimmomatic for testing from the command line
4 #
5 # Installation directory
6 TOP_DIR=$1
7 if [ -z "$TOP_DIR" ] ; then
8 echo Usage: $(basename $0) DIR
9 exit
10 fi
11 if [ -z "$(echo $TOP_DIR | grep ^/)" ] ; then
12 TOP_DIR=$(pwd)/$TOP_DIR
13 fi
14 if [ ! -d "$TOP_DIR" ] ; then
15 mkdir -p $TOP_DIR
16 fi
17 cd $TOP_DIR
18 # Trimmomatic 0.32
19 INSTALL_DIR=$TOP_DIR/trimmomatic/0.32
20 mkdir -p $INSTALL_DIR
21 wd=$(mktemp -d)
22 pushd $wd
23 wget -q http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
24 unzip -qq Trimmomatic-0.32.zip
25 mv Trimmomatic-0.32/trimmomatic-0.32.jar $INSTALL_DIR/
26 mv Trimmomatic-0.32/adapters/ $INSTALL_DIR/
27 popd
28 rm -rf $wd/*
29 rmdir $wd
30 # Make setup file
31 cat > trimmomatic/0.32/env.sh <<EOF
32 #!/bin/sh
33 # Source this to setup trimmomatic/0.32
34 echo Setting up Trimmomatic 0.32
35 export TRIMMOMATIC_DIR=$INSTALL_DIR
36 export TRIMMOMATIC_ADAPTERS_DIR=$INSTALL_DIR/adapters
37 #
38 EOF
39 ##
40 #