Add ShoRAH image

2024-11-21 09:26:04 +00:00 · 2021-09-07 12:27:57 -05:00 · 2021-09-07 12:27:57 -05:00 · 4b91b7cc91
commit 4b91b7cc91
parent 9a0114a0c5
2 changed files with 89 additions and 0 deletions
--- a/shorah/README.md
+++ b/shorah/README.md
@ -0,0 +1,18 @@
+# ShoRAH
+
+[![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/shorah)
+[![ShoRAH source](https://img.shields.io/static/v1?label=ShoRAH%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/cbg-ethz/shorah)
+[![Version 1.99.2](https://img.shields.io/static/v1?label=Latest%20version&message=1.99.2&color=yellowgreen&logo=linuxcontainers&style=flat-square)](https://cloud.sylabs.io/library/millironx/default/shorah)
+[![Docs](https://img.shields.io/static/v1?label=Docs&message=web&color=blue&style=flat-square)](https://github.com/cbg-ethz/shorah)
+[![Alpine base](https://img.shields.io/static/v1?label=Base%20image&message=Alpine&color=0d597f&logo=alpinelinux&style=flat-square)](https://www.alpinelinux.org/)
+
+ShoRAH is an open source project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools are written in different programming languages and provide error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.
+
+## Tools installed
+
+### ShoRAH
+
+- `shorah`
+- `b2w`
+- `diri_sampler`
+- `fil`
--- a/shorah/shorah.def
+++ b/shorah/shorah.def
@ -0,0 +1,71 @@
+Bootstrap: library
+From: millironx/default/htslib:1.13
+
+%post
+  # Install dependencies
+  apk add --no-cache python3 libcurl
+
+  # Install build dependencies
+  apk add --no-cache --virtual .build-deps py-pip g++ musl-dev make python3-dev boost-dev curl-dev
+
+  # Install python package dependencies
+  pip install --no-cache-dir biopython==1.79 numpy==1.21.2
+
+  # Make versioning easier
+  SHORAH_VERSION=1.99.2
+
+  # Download the source tarball and build
+  cd /tmp || exit 1
+  wget https://github.com/cbg-ethz/shorah/releases/download/v$SHORAH_VERSION/shorah-$SHORAH_VERSION.tar.bz2 -O shorah-$SHORAH_VERSION.tar.bz2
+  tar xjvf shorah-$SHORAH_VERSION.tar.bz2
+  cd shorah-$SHORAH_VERSION
+  ./configure
+  make
+  make install
+  cd .. || exit 1
+  rm -rf shorah-$SHORAH_VERSION*
+  cd || exit 1
+
+  # Cleanup build packages
+  apk del --no-cache .build-deps
+
+%test
+  test_command () {
+    if ! command -v "${1}"; then
+      echo "command ${1} not found!"
+      export FAILED_TESTS=1
+    fi
+  }
+
+  test_command bash
+  test_command ps
+  test_command shorah
+  test_command b2w
+  test_command diri_sampler
+  test_command fil
+
+  if [ -n "$FAILED_TESTS" ]; then
+    exit 1
+  fi
+
+%runscript
+  shorah "$@"
+
+%labels
+  Author 25492070+MillironX@users.noreply.github.com
+  SoftwareVersion 2.0.2
+  SingularityDefinitionVersion 1
+
+%help
+  ShoRAH
+  ======
+
+  ShoRAH is an open source project for the analysis of next generation
+  sequencing data. It is designed to analyse genetically heterogeneous samples.
+  Its tools are written in different programming languages and provide error
+  correction, haplotype reconstruction and estimation of the frequency of the
+  different genetic variants present in a mixed sample.
+
+  For more help, see
+  - <http://cbg-ethz.github.io/shorah>
+  - <https://github.com/MillironX/singularity-builds>