diff --git a/clique-snv/README.md b/clique-snv/README.md new file mode 100644 index 0000000..c8312c2 --- /dev/null +++ b/clique-snv/README.md @@ -0,0 +1,16 @@ +# CliqueSNV + +[![Container source](https://img.shields.io/static/v1?label=Container%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/MillironX/singularity-builds/tree/master/clique-snv) +[![CliqueSNV source](https://img.shields.io/static/v1?label=CliqueSNV%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/vtsyvina/CliqueSNV) +[![Version 2.0.2](https://img.shields.io/static/v1?label=Latest%20version&message=2.0.2&color=yellowgreen&logo=linuxcontainers&style=flat-square)](https://cloud.sylabs.io/library/millironx/default/clique-snv) +[![Docs](https://img.shields.io/static/v1?label=Docs&message=README&color=blue&style=flat-square)](https://github.com/vtsyvina/CliqueSNV/blob/master/README.md) +[![Alpine base](https://img.shields.io/static/v1?label=Base%20image&message=Alpine&color=0d597f&logo=alpinelinux&style=flat-square)](https://www.alpinelinux.org/) + +CliqueSNV can identify minority haplotypes based on extracting pairs of statistically linked mutations from noisy reads. + +## Tools installed + +### CliqueSNV + +- `java` +- `clique-snv` as alias for `java -jar clique-snv.jar ...` diff --git a/clique-snv/clique-snv.def b/clique-snv/clique-snv.def new file mode 100644 index 0000000..7889cfb --- /dev/null +++ b/clique-snv/clique-snv.def @@ -0,0 +1,57 @@ +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 + - + -