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singularity-builds/clique-snv/clique-snv.def

58 lines
1.2 KiB
Modula-2

Bootstrap: library
From: default/alpine:3.14.0
%post
# Install java
apk add --no-cache openjdk8 bash
# Make versioning easier
CLIQUE_VERSION=2.0.2
cd /opt
wget https://github.com/vtsyvina/CliqueSNV/archive/refs/tags/$CLIQUE_VERSION.tar.gz -O cliquesnv.tar.gz
tar xvzf cliquesnv.tar.gz
rm cliquesnv.tar.gz
cd
{
echo "#!/bin/bash"
echo "java -jar /opt/CliqueSNV-$CLIQUE_VERSION/clique-snv.jar \"\$@\""
} > /usr/bin/clique-snv
chmod +x /usr/bin/clique-snv
%test
test_command () {
if ! command -v "${1}"; then
echo "command ${1} not found!"
export FAILED_TESTS=1
fi
}
test_command bash
test_command ps
test_command java
test_command clique-snv
if [ -n "$FAILED_TESTS" ]; then
exit 1
fi
%runscript
clique-snv "$@"
%labels
Author 25492070+MillironX@users.noreply.github.com
SoftwareVersion 2.0.2
SingularityDefinitionVersion 1
%help
CliqueSNV
=========
CliqueSNV can identify minority haplotypes based on extracting pairs of
statistically linked mutations from noisy reads.
For more help, see
- <https://github.com/vtsyvina/CliqueSNV>
- <https://github.com/MillironX/singularity-builds>