singularity-builds/minimap_plus/minimap_plus.def

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1.7 KiB
Modula-2

Bootstrap: library
From: millironx/default/samtools:1.13
%post
# Get the actual dependencies
apk add --no-cache perl
# Get the build dependencies
apk add --no-cache --virtual .build-deps musl-dev g++ make zlib-dev
# Part 1: Install minimap2
# ========================
# Make versioning easier
MINIMAP2_VERSION='2.22'
# Download the source tarball and build
cd /tmp || exit 1
wget https://github.com/lh3/minimap2/releases/download/v$MINIMAP2_VERSION/minimap2-$MINIMAP2_VERSION.tar.bz2
tar xjvf minimap2-$MINIMAP2_VERSION.tar.bz2
cd minimap2-$MINIMAP2_VERSION || exit 1
make
install -D -m 0755 minimap2 -t /usr/bin
cd .. || exit 1
rm -rf minimap2-$MINIMAP2_VERSION*
cd || exit 1
# Part 2: Install samclip
SAMCLIP_VERSION='0.4.0'
cd /usr/bin || exit 1
wget https://raw.githubusercontent.com/tseemann/samclip/v$SAMCLIP_VERSION/samclip
chmod a+x samclip
cd || exit 1
# Cleanup build packages
apk del --no-cache .build-deps
%test
test_command () {
if ! command -v "${1}"; then
echo "command ${1} not found!"
export FAILED_TESTS=1
fi
}
test_command bash
test_command ps
test_command samtools
test_command minimap2
test_command samclip
if [ -n "$FAILED_TESTS" ]; then
exit 1
fi
%runscript
minimap2 "$@"
%labels
Author 25492070+MillironX@users.noreply.github.com
SoftwareVersion 2.22
SingularityDefinitionVersion 1
%help
minimap2
========
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA
sequences against a large reference database.
For more help, see
- <https://lh3.github.io/minimap2/>
- <https://github.com/lh3/minimap2>
- <https://github.com/MillironX/singularity-builds>