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recipe.scif
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recipe.scif
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%apprun samtools
exec /usr/bin/samtools "$@"
%appinstall samtools
apt-get update && apt-get install -y samtools
%apphelp samtools
This app provides Samtools suite
%applabels samtools
VERSION 1.7
URL http://www.htslib.org/
%apptest samtools
exec /usr/bin/samtools "$@"
%applabels bowtie
VERSION 2.2.7
%appinstall bowtie
curl -Lk -o bowtie.zip https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.7/bowtie2-2.2.7-linux-x86_64.zip/download
unzip bowtie.zip
mv bowtie2-2.2.7/* bin/
%apptest bowtie
exec /scif/bowtie/bin/bowtie2 "$@"
%applabels cufflinks
VERSION 2.2.1
%appinstall cufflinks
curl -Lk -o cufflinks.tar.gz http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
tar -xzvf cufflinks.tar.gz
mv cufflinks-2.2.1.Linux_x86_64/* bin/
%apptest cufflinks
exec /scif/cufflinks/bin/cufflinks "$@"
%applabels tophat
VERSION 2.1.0
%appenv tophat
PATH=/scif/apps/bowtie/bin:/usr/bin:$PATH
%appinstall tophat
curl -Lk -o tophat.tar.gz https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.Linux_x86_64.tar.gz
tar -xzvf tophat.tar.gz
mv tophat-2.1.0.Linux_x86_64/* bin/
%apptest tophat
exec /scif/tophat/bin/tophat "$@"