Add CliqueSNV

clique-snv/README.md

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+# 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 ...`

clique-snv/clique-snv.def

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+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>