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get-requirements.sh
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!/bin/bash
mainDir=$PWD
cd $mainDir
echo "Fetching bamtools 2.5.2 from https://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.2.tar.gz"
cd downloads-to-install/bamtools
curl -Lo v2.5.2.tar.gz https://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.2.tar.gz
if ! [ -f v2.5.2.tar.gz ];
then
echo "ERROR: Could not download bamtools! Check the link above and try to download it or a newer version (ending in .tar.gz) to place in downloads-to-install/bamtools. More information is available in the README."
exit 1
fi
cd $mainDir
echo "Fetching bowtie2 from https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.5.1/bowtie2-2.5.1-linux-x86_64.zip/download"
cd downloads-to-install/bowtie2
curl -Lo bowtie2-2.5.1-linux-x86_64.zip https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.5.1/bowtie2-2.5.1-linux-x86_64.zip/download
if ! [ -f bowtie2-2.5.1-linux-x86_64.zip ];
then
echo "ERROR: Could not download bowtie2! Check the link above and try to download it or a newer version (ending in .zip) to place in downloads-to-install/bowtie2. More information is available in the README."
exit 1
fi
cd $mainDir
echo "Fetching lofreq from https://github.com/CSB5/lofreq/raw/master/dist/lofreq_star-2.1.5_linux-x86-64.tgz"
cd downloads-to-install/lofreq
curl -Lo lofreq_star-2.1.5_linux-x86-64.tgz https://github.com/CSB5/lofreq/raw/master/dist/lofreq_star-2.1.5_linux-x86-64.tgz
if ! [ -f lofreq_star-2.1.5_linux-x86-64.tgz ];
then
echo "ERROR: Could not download lofreq! Check the link above and try to download it or a newer version (ending in .zgz) to place in downloads-to-install/lofreq. More information is available in the README."
exit 1
fi
cd $mainDir
echo "Fetching picard from https://github.com/broadinstitute/picard/releases/download/3.1.0/picard.jar"
cd downloads-to-install/picard
curl -Lo picard.jar https://github.com/broadinstitute/picard/releases/download/3.1.0/picard.jar
if ! [ -f picard.jar ];
then
echo "ERROR: Could not download picard! Check the link above and try to download it or a newer version (ending in .jar) to place in downloads-to-install/picard. More information is available in the README."
exit 1
fi
cd $mainDir
echo "Fetching samtools 1.18 from https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2"
cd downloads-to-install/samtools
curl -Lo samtools-1.18.tar.bz2 https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2
if ! [ -f samtools-1.18.tar.bz2 ];
then
echo "ERROR: Could not download samtools! Check the link above and try to download it or a newer version (ending in .tar.bz2) to place in downloads-to-install/samtools. More information is available in the README."
exit 1
fi
cd $mainDir
echo "The requirements should now be installed."