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install-wdl.sh
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install-wdl.sh
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#!/bin/bash
set -e -o pipefail
cached_fetch_jar_from_github () {
_github_org=$1
_tool_name=$2
_jar_version=$3
_jar_fname="$_tool_name-$_jar_version.jar"
if [ ! -f $CACHE_DIR/$_jar_fname ]; then
echo "Fetching $_jar_fname"
wget --quiet https://github.com/$_github_org/$_tool_name/releases/download/$_jar_version/$_jar_fname
mv $_jar_fname $CACHE_DIR
else
echo "Using cached $_jar_fname"
fi
ln -s $CACHE_DIR/$_jar_fname $_tool_name.jar
}
cached_fetch_jar_from_github broadinstitute wdltool 0.14
cached_fetch_jar_from_github broadinstitute cromwell 30.1
cached_fetch_jar_from_github dnanexus dxWDL 0.58.1
TGZ=dx-toolkit-v0.240.1-ubuntu-14.04-amd64.tar.gz
if [ ! -f $CACHE_DIR/$TGZ ]; then
echo "Fetching $TGZ"
wget --quiet https://wiki.dnanexus.com/images/files/$TGZ
mv $TGZ $CACHE_DIR
else
echo "Using cached $TGZ"
fi
tar -xzpf $CACHE_DIR/$TGZ
#echo "Fetching quayctl"
#wget --quiet https://github.com/coreos/quayctl/releases/download/v0.0.1/quayctl-linux-x64
#mv quayctl-linux-x64 quayctl
#chmod a+x quayctl