Add Samtools

samtools/README.md

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+# Samtools
+
+[![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/samtools)
+[![VarScan source](https://img.shields.io/static/v1?label=Samtools%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/samtools/samtools)
+[![Version 1.13](https://img.shields.io/static/v1?label=Latest%20version&message=1.13&color=yellowgreen&logo=linuxcontainers&style=flat-square)](https://cloud.sylabs.io/library/millironx/default/samtools)
+[![Docs](https://img.shields.io/static/v1?label=Docs&message=man/web&color=blue&style=flat-square)](https://www.htslib.org/doc/samtools.html)
+[![Alpine base](https://img.shields.io/static/v1?label=Base%20image&message=Alpine&color=0d597f&logo=alpinelinux&style=flat-square)](https://www.alpinelinux.org/)
+
+Samtools is a set of utilities that manipulate alignments in the SAM (Sequence Alignment/Map), BAM, and CRAM formats. It converts between the formats, does sorting, merging and indexing, and can retrieve reads in any regions swiftly.
+
+## Tools installed
+
+### samtools
+
+- `samtools`

samtools/samtools.def

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+Bootstrap: library
+From: default/alpine:3.14.0
+
+%post
+  # Get the actual dependencies
+  apk add --no-cache ncurses libbz2 xz zlib bash
+
+  # Get the build dependencies
+  apk add --no-cache --virtual .build-deps ncurses-dev musl-dev g++ make zlib-dev bzip2-dev xz-dev
+
+  # Make versioning easier
+  SAMTOOLS_VERSION='1.13'
+
+  # Download the source tarball and build
+  cd /tmp || exit 1
+  wget https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2
+  tar xjvf samtools-$SAMTOOLS_VERSION.tar.bz2
+  cd samtools-$SAMTOOLS_VERSION || exit 1
+  ./configure
+  make && make install
+  cd .. || exit 1
+  rm -rf samtools-$SAMTOOLS_VERSION*
+  cd || exit 1
+
+  # Cleanup build packages
+  apk del --no-cache .build-deps
+
+%test
+  test_command () {
+    if ! command -v "${1}"; then
+      echo "command ${1} not found!"
+      export FAILED_TESTS=1
+    fi
+  }
+
+  test_command bash
+  test_command ps
+  test_command samtools
+
+  if [ -n "$FAILED_TESTS" ]; then
+    exit 1
+  fi
+
+%runscript
+  samtools "$@"
+
+%labels
+  Author 25492070+MillironX@users.noreply.github.com
+  SoftwareVersion 1.13
+  SingularityDefinitionVersion 1
+
+%help
+  Samtools
+  ========
+
+  Samtools is a set of utilities that manipulate alignments in the SAM
+  (Sequence Alignment/Map), BAM, and CRAM formats. It converts between the
+  formats, does sorting, merging and indexing, and can retrieve reads in any
+  regions swiftly.
+
+  For more help, see
+  - <https://www.htslib.org/doc/samtools.html>
+  - <https://github.com/MillironX/singularity-builds>