mirror of
https://github.com/MillironX/singularity-builds.git
synced 2024-11-24 02:19:55 +00:00
74 lines
1.7 KiB
Modula-2
74 lines
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>
|