Re: [PR PATCH] [Updated] New package: samtools-1.13

[zzaba <zzaba@users.noreply.github.com>]

[-- Attachment #1: Type: text/plain, Size: 1488 bytes --]

There is an updated pull request by zzaba against master on the void-packages repository

https://github.com/zzaba/void-packages samtools
https://github.com/void-linux/void-packages/pull/32419

New package: samtools-1.13
<!-- Mark items with [x] where applicable -->

#### General
- [x] This is a new package and it conforms to the [quality requirements](https://github.com/void-linux/void-packages/blob/master/Manual.md#quality-requirements)

#### Have the results of the proposed changes been tested?
- [ ] I use the packages affected by the proposed changes on a regular basis and confirm this PR works for me
- [x] I generally don't use the affected packages but briefly tested this PR

<!--
If GitHub CI cannot be used to validate the build result (for example, if the
build is likely to take several hours), make sure to
[skip CI](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration).
When skipping CI, uncomment and fill out the following section.
Note: for builds that are likely to complete in less than 2 hours, it is not
acceptable to skip CI.
-->
 
#### Does it build and run successfully? 
I built this PR in like 15 mins for all archs.
- [x] I built this PR locally for my native architecture, (x86_64)
- [x] I built this PR locally for these architectures:
  - [x] aarch64-musl
  - [x] armv7l
  - [x] armv6l-musl


A patch file from https://github.com/void-linux/void-packages/pull/32419.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-samtools-32419.patch --]
[-- Type: text/x-diff, Size: 3920 bytes --]

From c3641ee1b61dac0e4425c81d932f017941f4b864 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Mon, 9 Aug 2021 03:31:21 +0400
Subject: [PATCH] New package: samtools-1.13

---
 common/shlibs             |  1 +
 srcpkgs/bcftools/template | 18 ++++++++++++++++++
 srcpkgs/htslib-devel      |  1 +
 srcpkgs/htslib/template   | 30 ++++++++++++++++++++++++++++++
 srcpkgs/samtools/template | 18 ++++++++++++++++++
 5 files changed, 68 insertions(+)
 create mode 100644 srcpkgs/bcftools/template
 create mode 120000 srcpkgs/htslib-devel
 create mode 100644 srcpkgs/htslib/template
 create mode 100644 srcpkgs/samtools/template

diff --git a/common/shlibs b/common/shlibs
index 278d2456072f..4f4d9cc4aa7c 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -4004,3 +4004,4 @@ liblhasa.so.0 lhasa-0.3.1_2
 libmt32emu.so.2 libmt32emu-2.5.1_1
 libqrtr-glib.so.0 libqrtr-glib-1.0.0_1
 libstemmer.so.2 libstemmer-2.1.0_1
+libhts.so.3 htslib-1.13_1
diff --git a/srcpkgs/bcftools/template b/srcpkgs/bcftools/template
new file mode 100644
index 000000000000..c0732f3510b5
--- /dev/null
+++ b/srcpkgs/bcftools/template
@@ -0,0 +1,18 @@
+# Template file for 'bcftools'
+pkgname=bcftools
+version=1.13
+revision=1
+build_style=configure
+configure_args="--prefix=/usr --with-htslib=system"
+makedepends="htslib-devel zlib-devel gsl-devel perl"
+short_desc="Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/${pkgname}/releases/download/${version}/${pkgname}-${version}.tar.bz2"
+checksum="13bfa1da2a5edda8fa51196a47a0b4afb3fef17516451e4f0e78477f3dd30b90"
+python_version=3
+
+post_install() {
+	vlicense LICENSE
+}
diff --git a/srcpkgs/htslib-devel b/srcpkgs/htslib-devel
new file mode 120000
index 000000000000..9786daad45dd
--- /dev/null
+++ b/srcpkgs/htslib-devel
@@ -0,0 +1 @@
+htslib
\ No newline at end of file
diff --git a/srcpkgs/htslib/template b/srcpkgs/htslib/template
new file mode 100644
index 000000000000..ea70357207c7
--- /dev/null
+++ b/srcpkgs/htslib/template
@@ -0,0 +1,30 @@
+# Template file for 'htslib'
+pkgname=htslib
+version=1.13
+revision=1
+build_style=configure
+configure_args="--prefix=/usr"
+makedepends="zlib-devel bzip2-devel liblzma-devel libcurl-devel openssl-devel"
+checkdepends="perl"
+short_desc="A C library for high-throughput sequencing data formats"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/${pkgname}/releases/download/${version}/${pkgname}-${version}.tar.bz2"
+checksum="f2407df9f97f0bb6b07656579e41a1ca5100464067b6b21bf962a2ea4b0efd65"
+
+post_install() {
+	vlicense LICENSE
+}
+
+htslib-devel_package() {
+	depends="${sourcepkg}>=${version}_${revision}"
+	short_desc+=" - development files"
+	pkg_install() {
+		vmove usr/include
+		vmove usr/lib/pkgconfig
+		vmove "usr/lib/*.a"
+		vmove "usr/lib/*.so"
+		vmove usr/share
+	}
+}
diff --git a/srcpkgs/samtools/template b/srcpkgs/samtools/template
new file mode 100644
index 000000000000..f179f13aba35
--- /dev/null
+++ b/srcpkgs/samtools/template
@@ -0,0 +1,18 @@
+# Template file for 'samtools'
+pkgname=samtools
+version=1.13
+revision=1
+build_style=configure
+configure_args="--prefix=/usr --with-htslib=system"
+makedepends="htslib-devel zlib-devel ncurses-devel"
+checkdepends="perl"
+short_desc="Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/${pkgname}/releases/download/${version}/${pkgname}-${version}.tar.bz2"
+checksum="616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60"
+
+post_install() {
+	vlicense LICENSE
+}