singularity-builds/samtools/samtools.def

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2021-08-17 16:21:23 +00:00
Bootstrap: library
From: default/alpine:3.14.0
%post
# Get the actual dependencies
apk add --no-cache ncurses libbz2 xz zlib bash
# Get the build dependencies
apk add --no-cache --virtual .build-deps ncurses-dev musl-dev g++ make zlib-dev bzip2-dev xz-dev
# Make versioning easier
SAMTOOLS_VERSION='1.13'
# Download the source tarball and build
cd /tmp || exit 1
wget https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2
tar xjvf samtools-$SAMTOOLS_VERSION.tar.bz2
cd samtools-$SAMTOOLS_VERSION || exit 1
./configure
make && make install
cd .. || exit 1
rm -rf samtools-$SAMTOOLS_VERSION*
cd || exit 1
# Cleanup build packages
apk del --no-cache .build-deps
%test
test_command () {
if ! command -v "${1}"; then
echo "command ${1} not found!"
export FAILED_TESTS=1
fi
}
test_command bash
test_command ps
test_command samtools
if [ -n "$FAILED_TESTS" ]; then
exit 1
fi
%runscript
samtools "$@"
%labels
Author 25492070+MillironX@users.noreply.github.com
SoftwareVersion 1.13
SingularityDefinitionVersion 1
%help
Samtools
========
Samtools is a set of utilities that manipulate alignments in the SAM
(Sequence Alignment/Map), BAM, and CRAM formats. It converts between the
formats, does sorting, merging and indexing, and can retrieve reads in any
regions swiftly.
For more help, see
- <https://www.htslib.org/doc/samtools.html>
- <https://github.com/MillironX/singularity-builds>