From 4b91b7cc9161ed99536efaf4d16a7060fd09d0af Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 7 Sep 2021 12:27:57 -0500
Subject: [PATCH] Add ShoRAH image

---
 shorah/README.md  | 18 ++++++++++++
 shorah/shorah.def | 71 +++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 89 insertions(+)
 create mode 100644 shorah/README.md
 create mode 100644 shorah/shorah.def

diff --git a/shorah/README.md b/shorah/README.md
new file mode 100644
index 0000000..73a2009
--- /dev/null
+++ 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`
diff --git a/shorah/shorah.def b/shorah/shorah.def
new file mode 100644
index 0000000..b0d4310
--- /dev/null
+++ 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>