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Added version 1.15.1
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‎1.15.1/Singularity

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Bootstrap: docker
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From: alpine:edge
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%labels
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MAINTAINER icaoberg
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EMAIL [email protected]
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SUPPORT [email protected]
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REPOSITORY https://github.com/pscedu/singularity-samtools
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COPYRIGHT Copyright © 2021 Pittsburgh Supercomputing Center. All Rights Reserved.
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VERSION 1.15.1
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%post
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apk update # Ensure the package list is up to date
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apk add autoconf automake make gcc musl-dev perl bash zlib-dev bzip2-dev xz-dev curl-dev libressl-dev ncurses-dev wget
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wget -nc https://github.com/samtools/samtools/releases/download/1.15.1/samtools-1.15.1.tar.bz2
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tar -xvf samtools-1.15.1.tar.bz2 && rm -f samtools-1.15.1.tar.bz2
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mv samtools-1.15.1 /opt/
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cd /opt/samtools-1.15.1
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./configure
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make
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make install

‎1.15.1/ace2sam

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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=ace2sam
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DIRECTORY=$(dirname $0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d $PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B $PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=$OPTIONS" -B /local"
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fi
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singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

‎1.15.1/blast2sam.pl

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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=blast2sam.pl
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DIRECTORY=$(dirname $0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d $PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B $PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=$OPTIONS" -B /local"
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fi
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singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

‎1.15.1/bowtie2sam.pl

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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=bowtie2sam.pl
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DIRECTORY=$(dirname $0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d $PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B $PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=$OPTIONS" -B /local"
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fi
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singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

‎1.15.1/build.sh

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#!/bin/bash
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# Copyright © 2021 Pittsburgh Supercomputing Center.
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# All Rights Reserved.
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IMAGE=singularity-samtools-1.15.1.sif
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DEFINITION=Singularity
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if [ -f $IMAGE ]; then
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rm -fv $IMAGE
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fi
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sudo singularity build $IMAGE $DEFINITION
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if [ -f $IMAGE ]; then
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exit 0
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else
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exit 1
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fi

‎1.15.1/export2sam.pl

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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=export2sam.pl
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DIRECTORY=$(dirname $0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d $PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B $PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=$OPTIONS" -B /local"
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fi
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singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

‎1.15.1/fasta-sanitize.pl

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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=fasta-sanitize.pl
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DIRECTORY=$(dirname $0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d $PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B $PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=$OPTIONS" -B /local"
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fi
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singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

‎1.15.1/generate_binaries.sh

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#!/bin/bash
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# Copyright © 2021 Pittsburgh Supercomputing Center.
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# All Rights Reserved.
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TOOLS=(ace2sam md5fa samtools.pl
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blast2sam.pl md5sum-lite seq_cache_populate.pl
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bowtie2sam.pl novo2sam.pl soap2sam.pl
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export2sam.pl plot-ampliconstats wgsim
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fasta-sanitize.pl plot-bamstats wgsim_eval.pl
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interpolate_sam.pl psl2sam.pl zoom2sam.pl
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maq2sam-long sam2vcf.pl
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maq2sam-short samtools)
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cat << EOF > template
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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=TOOL_NAME
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DIRECTORY=\$(dirname \$0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d \$PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B \$PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=\$OPTIONS" -B /local"
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fi
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singularity exec \$OPTIONS \$DIRECTORY/singularity-\$PACKAGE-\$VERSION.sif \$TOOL "\$@"
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EOF
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for TOOL in "${TOOLS[@]}"
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do
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echo "* "$TOOL
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cp template $TOOL
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sed -i "s/TOOL_NAME/$TOOL/g" $TOOL
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chmod +x $TOOL
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git add $TOOL
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done
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rm -f template

‎1.15.1/interpolate_sam.pl

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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=interpolate_sam.pl
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DIRECTORY=$(dirname $0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d $PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B $PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=$OPTIONS" -B /local"
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fi
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singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

‎1.15.1/maq2sam-long

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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=maq2sam-long
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DIRECTORY=$(dirname $0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d $PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B $PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=$OPTIONS" -B /local"
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fi
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singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

‎1.15.1/maq2sam-short

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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=maq2sam-short
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DIRECTORY=$(dirname $0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d $PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B $PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=$OPTIONS" -B /local"
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fi
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singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

‎1.15.1/md5fa

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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=md5fa
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DIRECTORY=$(dirname $0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d $PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B $PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=$OPTIONS" -B /local"
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fi
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singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

‎1.15.1/md5sum-lite

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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=md5sum-lite
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DIRECTORY=$(dirname $0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d $PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B $PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=$OPTIONS" -B /local"
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fi
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singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

‎1.15.1/modulefile.lua

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--
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-- samtools 1.15.1 modulefile
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--
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-- "URL: https://www.psc.edu/resources/software"
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-- "Category: Biological Sciences"
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-- "Description: Samtools is a suite of programs for interacting with high-throughput sequencing data."
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-- "Keywords: singularity bioinformatics"
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whatis("Name: samtools")
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whatis("Version: 1.15.1")
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whatis("Category: Biological Sciences")
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whatis("URL: https://www.psc.edu/resources/software")
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whatis("Description: samtools is a suite of programs for interacting with high-throughput sequencing data.")
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help([[
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samtools is a suite of programs for interacting with high-throughput sequencing data.
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To load the module type
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> module load samtools/1.15.1
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To unload the module type
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> module unload samtools/1.15.1
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Documentation
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-------------
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For help, type
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> samtools --help
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Tools included in this module are
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* ace2sam
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* md5fa
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* samtools.pl
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* blast2sam.pl
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* md5sum-lite
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* seq_cache_populate.pl
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* bowtie2sam.pl
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* novo2sam.pl
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* soap2sam.pl
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* export2sam.pl
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* plot-ampliconstats
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* wgsim
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* fasta-sanitize.pl
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* plot-bamstats
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* wgsim_eval.pl
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* interpolate_sam.pl
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* psl2sam.pl
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* zoom2sam.pl
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* maq2sam-long
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* sam2vcf.pl
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* maq2sam-short
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* samtools
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]])
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local package = "samtools"
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local version = "1.15.1"
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local base = pathJoin("/opt/packages",package,version)
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prepend_path("PATH", base)

‎1.15.1/novo2sam.pl

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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=novo2sam.pl
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DIRECTORY=$(dirname $0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d $PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B $PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=$OPTIONS" -B /local"
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fi
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singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

‎1.15.1/plot-ampliconstats

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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=plot-ampliconstats
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DIRECTORY=$(dirname $0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d $PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B $PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=$OPTIONS" -B /local"
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fi
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singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

‎1.15.1/plot-bamstats

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#!/bin/bash
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VERSION=1.15.1
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PACKAGE=samtools
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TOOL=plot-bamstats
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DIRECTORY=$(dirname $0)
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PERSISTENT_FILE_STORAGE=/ocean
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if [ -d $PERSISTENT_FILE_STORAGE ]; then
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OPTIONS="-B $PERSISTENT_FILE_STORAGE"
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fi
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if [ -d /local ]; then
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OPTIONS=$OPTIONS" -B /local"
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fi
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singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

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