Mercurial > repos > pjbriggs > trimmomatic
diff install_tool_deps.sh @ 3:f8a9a5eaca8a draft
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
| author | pjbriggs |
|---|---|
| date | Wed, 23 Sep 2015 08:59:23 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/install_tool_deps.sh Wed Sep 23 08:59:23 2015 -0400 @@ -0,0 +1,40 @@ +#!/bin/bash +# +# Install dependencies for Trimmomatic for testing from the command line +# +# Installation directory +TOP_DIR=$1 +if [ -z "$TOP_DIR" ] ; then + echo Usage: $(basename $0) DIR + exit +fi +if [ -z "$(echo $TOP_DIR | grep ^/)" ] ; then + TOP_DIR=$(pwd)/$TOP_DIR +fi +if [ ! -d "$TOP_DIR" ] ; then + mkdir -p $TOP_DIR +fi +cd $TOP_DIR +# Trimmomatic 0.32 +INSTALL_DIR=$TOP_DIR/trimmomatic/0.32 +mkdir -p $INSTALL_DIR +wd=$(mktemp -d) +pushd $wd +wget -q http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip +unzip -qq Trimmomatic-0.32.zip +mv Trimmomatic-0.32/trimmomatic-0.32.jar $INSTALL_DIR/ +mv Trimmomatic-0.32/adapters/ $INSTALL_DIR/ +popd +rm -rf $wd/* +rmdir $wd +# Make setup file +cat > trimmomatic/0.32/env.sh <<EOF +#!/bin/sh +# Source this to setup trimmomatic/0.32 +echo Setting up Trimmomatic 0.32 +export TRIMMOMATIC_DIR=$INSTALL_DIR +export TRIMMOMATIC_ADAPTERS_DIR=$INSTALL_DIR/adapters +# +EOF +## +#