From 0362a4b0375718a6b1036f1ce454d833c8dce390 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 7 Sep 2021 09:47:43 -0500
Subject: [PATCH] Add HTSlib image

---
 htslib/README.md  | 13 +++++++++++
 htslib/htslib.def | 57 +++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 70 insertions(+)
 create mode 100644 htslib/README.md
 create mode 100644 htslib/htslib.def

diff --git a/htslib/README.md b/htslib/README.md
new file mode 100644
index 0000000..2b1c309
--- /dev/null
+++ b/htslib/README.md
@@ -0,0 +1,13 @@
+# HTSLib
+
+[![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/htslib)
+[![VarScan source](https://img.shields.io/static/v1?label=HTSlib%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/samtools/htslib)
+[![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/htslib)
+[![Docs](https://img.shields.io/static/v1?label=Docs&message=web&color=blue&style=flat-square)](https://www.htslib.org/)
+[![Alpine base](https://img.shields.io/static/v1?label=Base%20image&message=Alpine&color=0d597f&logo=alpinelinux&style=flat-square)](https://www.alpinelinux.org/)
+
+HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools.
+
+## Tools installed
+
+none
diff --git a/htslib/htslib.def b/htslib/htslib.def
new file mode 100644
index 0000000..5655d12
--- /dev/null
+++ b/htslib/htslib.def
@@ -0,0 +1,57 @@
+Bootstrap: library
+From: default/alpine:3.14.0
+
+%post
+  # Get the actual dependencies
+  apk add --no-cache zlib bash
+
+  # Get the build dependencies
+  apk add --no-cache --virtual .build-deps musl-dev g++ make zlib-dev bzip2-dev xz-dev curl-dev
+
+  # Make versioning easier
+  HTSLIB_VERSION='1.13'
+
+  # Download the source tarball and build
+  cd /tmp || exit 1
+  wget https://github.com/samtools/htslib/releases/download/$HTSLIB_VERSION/htslib-$HTSLIB_VERSION.tar.bz2
+  tar xjvf htslib-$HTSLIB_VERSION.tar.bz2
+  cd htslib-$HTSLIB_VERSION || exit 1
+  make && make install
+  cd .. || exit 1
+  rm -rf htslib-$SAMTOOLS_VERSION*
+  cd || exit 1
+
+  # Cleanup build packages
+  apk del --no-cache .build-deps
+
+%test
+  test_command () {
+    if ! command -v "${1}"; then
+      echo "command ${1} not found!"
+      export FAILED_TESTS=1
+    fi
+  }
+
+  test_command bash
+  test_command ps
+
+  if [ -n "$FAILED_TESTS" ]; then
+    exit 1
+  fi
+
+%labels
+  Author 25492070+MillironX@users.noreply.github.com
+  SoftwareVersion 1.13
+  SingularityDefinitionVersion 1
+
+%help
+  HTSlib
+  ======
+
+  HTSlib is an implementation of a unified C library for accessing common file
+  formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data,
+  and is the core library used by samtools and bcftools.
+
+  For more help, see
+  - <https://www.htslib.org>
+  - <https://github.com/MillironX/singularity-builds>