[PR PATCH] New package: samtools-1.13

[PR PATCH] New package: samtools-1.13

[zzaba]

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There is a new 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

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#### Does it build and run successfully? 
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- [ ] I built this PR locally for my native architecture, (ARCH-LIBC)
- [ ] I built this PR locally for these architectures (if supported. mark crossbuilds):
  - [ ] aarch64-musl
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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 --]
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From 78dcf9b555fa5ae2c91f68228ea4fe27e08c49ad Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Mon, 9 Aug 2021 02:06:46 +0400
Subject: [PATCH] New package: samtools-1.13

---
 srcpkgs/samtools/template | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 srcpkgs/samtools/template

diff --git a/srcpkgs/samtools/template b/srcpkgs/samtools/template
new file mode 100644
index 000000000000..ab776bc8078a
--- /dev/null
+++ b/srcpkgs/samtools/template
@@ -0,0 +1,17 @@
+# Template file for 'samtools'
+pkgname=samtools
+version=1.13
+revision=1
+wrksrc="samtools-${version}"
+build_style=gnu-configure
+makedepends="zlib-devel bzip2-devel liblzma-devel libcurl-devel openssl-devel ncurses-devel"
+short_desc="Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/samtools/releases/download/${version}/samtools-${version}.tar.bz2"
+checksum="616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60"
+
+post_install() {
+	vlicense LICENSE
+}

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

[zzaba]

[-- 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

<!--
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When skipping CI, uncomment and fill out the following section.
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#### 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: 1155 bytes --]

From 9916a22d687c3dcc74c926a4df0e862256f5a1f5 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Mon, 9 Aug 2021 02:06:46 +0400
Subject: [PATCH] New package: samtools-1.13

---
 srcpkgs/samtools/template | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 srcpkgs/samtools/template

diff --git a/srcpkgs/samtools/template b/srcpkgs/samtools/template
new file mode 100644
index 000000000000..ab776bc8078a
--- /dev/null
+++ b/srcpkgs/samtools/template
@@ -0,0 +1,17 @@
+# Template file for 'samtools'
+pkgname=samtools
+version=1.13
+revision=1
+wrksrc="samtools-${version}"
+build_style=gnu-configure
+makedepends="zlib-devel bzip2-devel liblzma-devel libcurl-devel openssl-devel ncurses-devel"
+short_desc="Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/samtools/releases/download/${version}/samtools-${version}.tar.bz2"
+checksum="616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60"
+
+post_install() {
+	vlicense LICENSE
+}

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

[zzaba]

[-- 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
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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
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#### 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: 1160 bytes --]

From a2ecc918a9bb5e5901235d4bbfe3d20108218df5 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Mon, 9 Aug 2021 02:06:46 +0400
Subject: [PATCH] New package: samtools-1.13

---
 srcpkgs/samtools/template | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 srcpkgs/samtools/template

diff --git a/srcpkgs/samtools/template b/srcpkgs/samtools/template
new file mode 100644
index 000000000000..ec0111b058d9
--- /dev/null
+++ b/srcpkgs/samtools/template
@@ -0,0 +1,17 @@
+# Template file for 'samtools'
+pkgname=samtools
+version=1.13
+revision=1
+wrksrc="samtools-${version}"
+build_style=gnu-configure
+makedepends="zlib-devel bzip2-devel liblzma-devel libcurl-devel openssl-devel ncurses-devel perl"
+short_desc="Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/samtools/releases/download/${version}/samtools-${version}.tar.bz2"
+checksum="616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60"
+
+post_install() {
+	vlicense LICENSE
+}

Re: New package: samtools-1.13

[jmarshall]

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New comment by jmarshall on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#issuecomment-895210185

Comment:
Is there a reason you are building samtools using the copy of htslib bundled within the source tarball, rather than configuring your samtools package with `--with-htslib=system` and having it depend on your proposed htslib package?

Re: New package: samtools-1.13

[zzaba]

[-- Attachment #1: Type: text/plain, Size: 391 bytes --]

New comment by zzaba on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#issuecomment-895357503

Comment:
I couldn't figure out what the pull request should've looked like in that case, as proposed bcftools can also be configured with the same option, so I'd have to submit a pull request containing all three together which is, as I understood, discouraged.

Re: New package: samtools-1.13

[zzaba]

[-- Attachment #1: Type: text/plain, Size: 447 bytes --]

New comment by zzaba on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#issuecomment-895357503

Comment:
I couldn't figure out what the pull request should've looked like in that case, as proposed bcftools can also be configured with the same option and htslib should be split into htslib and htslib-devel, so I'd have to submit a pull request containing all four together which is, as I understood, discouraged. 

Re: New package: samtools-1.13

[paper42]

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New comment by paper42 on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#issuecomment-895387986

Comment:
> I'd have to submit a pull request containing all four together which is, as I understood, discouraged.

It's all about being simpler to review. Smaller independent pull requests are simpler to review, but when there are dependencies between them, it's much simpler to review one bigger PR.

htslib-devel would be a subpackage, not a full package

Re: New package: samtools-1.13

[zzaba]

[-- Attachment #1: Type: text/plain, Size: 181 bytes --]

New comment by zzaba on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#issuecomment-895389263

Comment:
Should I close these and open new big one?

Re: New package: samtools-1.13

[paper42]

[-- Attachment #1: Type: text/plain, Size: 168 bytes --]

New comment by paper42 on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#issuecomment-895400834

Comment:
You can repurpose this one.

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

[zzaba]

[-- 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
+}

Re: New package: samtools-1.13

[abenson]

[-- Attachment #1: Type: text/plain, Size: 182 bytes --]

New comment by abenson on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#issuecomment-895556294

Comment:
Each template should have its own commit.

Re: New package: samtools-1.13

[zzaba]

[-- Attachment #1: Type: text/plain, Size: 399 bytes --]

New comment by zzaba on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#issuecomment-895557901

Comment:
samtools and bcftools both depend on htslib so I'm pulling them together. Some tests on 32 bit architectures are expected to fail because of the floating number nature. I've contacted upstream about that here -> https://github.com/samtools/samtools/issues/1478

Re: New package: samtools-1.13

[paper42]

[-- Attachment #1: Type: text/plain, Size: 288 bytes --]

New comment by paper42 on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#issuecomment-895559731

Comment:
> samtools and bcftools both depend on htslib so I'm pulling them together

together in the same PR, but you can still have multiple commits here

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

[zzaba]

[-- 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: 4652 bytes --]

From b1878c9100c908f0ce31ec61fa0f7151d51a4843 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Tue, 10 Aug 2021 01:26:33 +0400
Subject: [PATCH 1/4] New package: samtools-1.13

---
 srcpkgs/samtools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/samtools/template

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
+}

From bb9035a8e97f3c992ff60ddab44af32be2f53461 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Tue, 10 Aug 2021 01:26:38 +0400
Subject: [PATCH 2/4] New package: bcftools-1.13

---
 srcpkgs/bcftools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/bcftools/template

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
+}

From 17eb2dd23afa9d187617a48621ddd360672fc06f Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Tue, 10 Aug 2021 01:26:50 +0400
Subject: [PATCH 3/4] New package: htslib-1.13

---
 srcpkgs/htslib-devel    |  1 +
 srcpkgs/htslib/template | 30 ++++++++++++++++++++++++++++++
 2 files changed, 31 insertions(+)
 create mode 120000 srcpkgs/htslib-devel
 create mode 100644 srcpkgs/htslib/template

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
+	}
+}

From b203afab824875a90bf1d8f726f21890d826312c Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Tue, 10 Aug 2021 01:27:40 +0400
Subject: [PATCH 4/4] Resolve libhts.so.3 to htslib-1.13_1

---
 common/shlibs | 1 +
 1 file changed, 1 insertion(+)

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

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

[zzaba]

[-- 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: 4409 bytes --]

From b1878c9100c908f0ce31ec61fa0f7151d51a4843 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Tue, 10 Aug 2021 01:26:33 +0400
Subject: [PATCH 1/3] New package: samtools-1.13

---
 srcpkgs/samtools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/samtools/template

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
+}

From bb9035a8e97f3c992ff60ddab44af32be2f53461 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Tue, 10 Aug 2021 01:26:38 +0400
Subject: [PATCH 2/3] New package: bcftools-1.13

---
 srcpkgs/bcftools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/bcftools/template

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
+}

From d408625f9b6efffea5e67fe95b416884d3c8a943 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Tue, 10 Aug 2021 01:26:50 +0400
Subject: [PATCH 3/3] New package: htslib-1.13

---
 common/shlibs           |  1 +
 srcpkgs/htslib-devel    |  1 +
 srcpkgs/htslib/template | 30 ++++++++++++++++++++++++++++++
 3 files changed, 32 insertions(+)
 create mode 120000 srcpkgs/htslib-devel
 create mode 100644 srcpkgs/htslib/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/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
+	}
+}

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

[zzaba]

[-- 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: 4360 bytes --]

From c050117c426a4bb7f25fcf2192c9a178c7eb250c Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Tue, 10 Aug 2021 02:17:28 +0400
Subject: [PATCH 1/3] New package: samtools-1.13

---
 srcpkgs/samtools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/samtools/template

diff --git a/srcpkgs/samtools/template b/srcpkgs/samtools/template
new file mode 100644
index 000000000000..b03ca2c7b2f4
--- /dev/null
+++ b/srcpkgs/samtools/template
@@ -0,0 +1,18 @@
+# Template file for 'samtools'
+pkgname=samtools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--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
+}

From 30acf282e85c660201d5ab44426379c625acb85e Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Tue, 10 Aug 2021 02:17:32 +0400
Subject: [PATCH 2/3] New package: bcftools-1.13

---
 srcpkgs/bcftools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/bcftools/template

diff --git a/srcpkgs/bcftools/template b/srcpkgs/bcftools/template
new file mode 100644
index 000000000000..864940989ee9
--- /dev/null
+++ b/srcpkgs/bcftools/template
@@ -0,0 +1,18 @@
+# Template file for 'bcftools'
+pkgname=bcftools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--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
+}

From 3f332edbb6437b80afcb9f8b642b1e0a6d198024 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Tue, 10 Aug 2021 02:17:37 +0400
Subject: [PATCH 3/3] New package: htslib-1.13

---
 common/shlibs           |  1 +
 srcpkgs/htslib-devel    |  1 +
 srcpkgs/htslib/template | 29 +++++++++++++++++++++++++++++
 3 files changed, 31 insertions(+)
 create mode 120000 srcpkgs/htslib-devel
 create mode 100644 srcpkgs/htslib/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/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..32e7fc777fea
--- /dev/null
+++ b/srcpkgs/htslib/template
@@ -0,0 +1,29 @@
+# Template file for 'htslib'
+pkgname=htslib
+version=1.13
+revision=1
+build_style=gnu-configure
+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
+	}
+}

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

[zzaba]

[-- 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: 4322 bytes --]

From c050117c426a4bb7f25fcf2192c9a178c7eb250c Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Tue, 10 Aug 2021 02:17:28 +0400
Subject: [PATCH 1/3] New package: samtools-1.13

---
 srcpkgs/samtools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/samtools/template

diff --git a/srcpkgs/samtools/template b/srcpkgs/samtools/template
new file mode 100644
index 000000000000..b03ca2c7b2f4
--- /dev/null
+++ b/srcpkgs/samtools/template
@@ -0,0 +1,18 @@
+# Template file for 'samtools'
+pkgname=samtools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--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
+}

From 20a29b926d77458831186adefff01b2264a49cc9 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Tue, 10 Aug 2021 02:42:32 +0400
Subject: [PATCH 2/3] New package: bcftools-1.13

---
 srcpkgs/bcftools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/bcftools/template

diff --git a/srcpkgs/bcftools/template b/srcpkgs/bcftools/template
new file mode 100644
index 000000000000..04fdd55b32d3
--- /dev/null
+++ b/srcpkgs/bcftools/template
@@ -0,0 +1,18 @@
+# Template file for 'bcftools'
+pkgname=bcftools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--with-htslib=system"
+makedepends="htslib-devel zlib-devel gsl-devel perl"
+short_desc="Read/write BCF2/VCF/gVCF files and call/filter/sum SNP and short indels"
+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
+}

From b3a645ae01f8ffba8aa8d6cd17793ed6a61de840 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Tue, 10 Aug 2021 02:42:38 +0400
Subject: [PATCH 3/3] New package: htslib-1.13

---
 common/shlibs           |  1 +
 srcpkgs/htslib-devel    |  1 +
 srcpkgs/htslib/template | 29 +++++++++++++++++++++++++++++
 3 files changed, 31 insertions(+)
 create mode 120000 srcpkgs/htslib-devel
 create mode 100644 srcpkgs/htslib/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/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..fd977b9e21a7
--- /dev/null
+++ b/srcpkgs/htslib/template
@@ -0,0 +1,29 @@
+# Template file for 'htslib'
+pkgname=htslib
+version=1.13
+revision=1
+build_style=gnu-configure
+makedepends="zlib-devel bzip2-devel liblzma-devel libcurl-devel openssl-devel"
+checkdepends="perl"
+short_desc="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
+	}
+}

Re: [PR REVIEW] New package: samtools-1.13

[ericonr]

[-- Attachment #1: Type: text/plain, Size: 157 bytes --]

New review comment by ericonr on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686224056

Comment:
Same here.

Re: [PR REVIEW] New package: samtools-1.13

[ericonr]

[-- Attachment #1: Type: text/plain, Size: 197 bytes --]

New review comment by ericonr on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686223760

Comment:
Please expand `pkgname` at least before "releases"

Re: [PR REVIEW] New package: samtools-1.13

[ericonr]

[-- Attachment #1: Type: text/plain, Size: 157 bytes --]

New review comment by ericonr on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686224943

Comment:
Same here.

Re: [PR REVIEW] New package: samtools-1.13

[ericonr]

[-- Attachment #1: Type: text/plain, Size: 232 bytes --]

New review comment by ericonr on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686224456

Comment:
I'd say "read/write/edit/index/view SAM/BAM/CRAM files" is clearer? or "format files"

Re: [PR REVIEW] New package: samtools-1.13

[zzaba]

[-- Attachment #1: Type: text/plain, Size: 212 bytes --]

New review comment by zzaba on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686281039

Comment:
I'd rather preserve the [original wording](https://www.htslib.org).

Re: [PR REVIEW] New package: samtools-1.13

[zzaba]

[-- Attachment #1: Type: text/plain, Size: 165 bytes --]

New review comment by zzaba on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686281612

Comment:
Sure thing, but why?

Re: [PR REVIEW] New package: samtools-1.13

[paper42]

[-- Attachment #1: Type: text/plain, Size: 393 bytes --]

New review comment by paper42 on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686304994

Comment:
* it doesn't usually save any characters
* if $pkgname changes for some reason (like libhandy and libhandy1 which is 1 library in different versions), we might want to keep the same distfiles URL

and probably more reasons I don't remember now

Re: [PR REVIEW] New package: samtools-1.13

[zzaba]

[-- Attachment #1: Type: text/plain, Size: 215 bytes --]

New review comment by zzaba on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686309264

Comment:
Should I change all occurrences of $pkgname then? What about $version?

Re: [PR REVIEW] New package: samtools-1.13

[paper42]

[-- Attachment #1: Type: text/plain, Size: 419 bytes --]

New review comment by paper42 on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686318070

Comment:
yes, please remove all mentions of $pkgname in $distfiles

When updating a package, we want to keep using the same distfiles string, just bump the version and fix the checksum, so having only one place where we need to change the version is very useful, don't remove it.

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

[zzaba]

[-- 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: 4300 bytes --]

From 8349f479562f32361632bbb7b2ea7bb736f054cd Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 01:01:43 +0400
Subject: [PATCH 1/3] New package: htslib-1.13

---
 common/shlibs           |  1 +
 srcpkgs/htslib-devel    |  1 +
 srcpkgs/htslib/template | 29 +++++++++++++++++++++++++++++
 3 files changed, 31 insertions(+)
 create mode 120000 srcpkgs/htslib-devel
 create mode 100644 srcpkgs/htslib/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/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..9a3b1413caf7
--- /dev/null
+++ b/srcpkgs/htslib/template
@@ -0,0 +1,29 @@
+# Template file for 'htslib'
+pkgname=htslib
+version=1.13
+revision=1
+build_style=gnu-configure
+makedepends="zlib-devel bzip2-devel liblzma-devel libcurl-devel openssl-devel"
+checkdepends="perl"
+short_desc="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/htslib/releases/download/${version}/htslib-${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
+	}
+}

From 369cf9b1adc84f2c74a78d31ab2f7d802924b2a2 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 01:02:08 +0400
Subject: [PATCH 2/3] New package: bcftools-1.13

---
 srcpkgs/bcftools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/bcftools/template

diff --git a/srcpkgs/bcftools/template b/srcpkgs/bcftools/template
new file mode 100644
index 000000000000..b15b853cfa97
--- /dev/null
+++ b/srcpkgs/bcftools/template
@@ -0,0 +1,18 @@
+# Template file for 'bcftools'
+pkgname=bcftools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--with-htslib=system"
+makedepends="htslib-devel zlib-devel gsl-devel perl"
+short_desc="Read/write BCF2/VCF/gVCF files and call/filter/sum SNP and short indels"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/bcftools/releases/download/${version}/bcftools-${version}.tar.bz2"
+checksum=13bfa1da2a5edda8fa51196a47a0b4afb3fef17516451e4f0e78477f3dd30b90
+python_version=3
+
+post_install() {
+	vlicense LICENSE
+}

From 553cdf80c74fdf87774359319e5333491fa6635c Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 01:02:12 +0400
Subject: [PATCH 3/3] New package: samtools-1.13

---
 srcpkgs/samtools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/samtools/template

diff --git a/srcpkgs/samtools/template b/srcpkgs/samtools/template
new file mode 100644
index 000000000000..49461ff194c0
--- /dev/null
+++ b/srcpkgs/samtools/template
@@ -0,0 +1,18 @@
+# Template file for 'samtools'
+pkgname=samtools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--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/samtools/releases/download/${version}/samtools-${version}.tar.bz2"
+checksum=616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60
+
+post_install() {
+	vlicense LICENSE
+}

Re: [PR REVIEW] New package: samtools-1.13

[ericonr]

[-- Attachment #1: Type: text/plain, Size: 282 bytes --]

New review comment by ericonr on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686437698

Comment:
I don't think using "reading" instead of "read" fits well for a package description... Would you agree to changing the verbs, at least?

Re: [PR REVIEW] New package: samtools-1.13

[jmarshall]

[-- Attachment #1: Type: text/plain, Size: 292 bytes --]

New review comment by jmarshall on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686631084

Comment:
If you're making the package depend on `gsl-devel`, then you should activate the GSL-using functionality by configuring with `--enable-libgsl`.

Re: [PR REVIEW] New package: samtools-1.13

[jmarshall]

[-- Attachment #1: Type: text/plain, Size: 298 bytes --]

New review comment by jmarshall on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686631084

Comment:
If you're making the package build-depend on `gsl-devel`, then you should activate the GSL-using functionality by configuring with `--enable-libgsl`.

Re: [PR REVIEW] New package: samtools-1.13

[zzaba]

[-- Attachment #1: Type: text/plain, Size: 192 bytes --]

New review comment by zzaba on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686721018

Comment:
Thanks! Didn't notice that. Same goes for perl.

Re: [PR REVIEW] New package: samtools-1.13

[zzaba]

[-- Attachment #1: Type: text/plain, Size: 149 bytes --]

New review comment by zzaba on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#discussion_r686721207

Comment:
Okay

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

[zzaba]

[-- 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: 4323 bytes --]

From 9ecc5c74ec830cfe4498f8be2f151f6fdc43945e Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 15:05:37 +0400
Subject: [PATCH 1/3] New package: htslib-1.13

---
 common/shlibs           |  1 +
 srcpkgs/htslib-devel    |  1 +
 srcpkgs/htslib/template | 29 +++++++++++++++++++++++++++++
 3 files changed, 31 insertions(+)
 create mode 120000 srcpkgs/htslib-devel
 create mode 100644 srcpkgs/htslib/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/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..9a3b1413caf7
--- /dev/null
+++ b/srcpkgs/htslib/template
@@ -0,0 +1,29 @@
+# Template file for 'htslib'
+pkgname=htslib
+version=1.13
+revision=1
+build_style=gnu-configure
+makedepends="zlib-devel bzip2-devel liblzma-devel libcurl-devel openssl-devel"
+checkdepends="perl"
+short_desc="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/htslib/releases/download/${version}/htslib-${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
+	}
+}

From bc50b4a5e3ff961f7b8f5f6524a1bed9d49f9574 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 15:05:56 +0400
Subject: [PATCH 2/3] New package: bcftools-1.13

---
 srcpkgs/bcftools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/bcftools/template

diff --git a/srcpkgs/bcftools/template b/srcpkgs/bcftools/template
new file mode 100644
index 000000000000..ea74811827e4
--- /dev/null
+++ b/srcpkgs/bcftools/template
@@ -0,0 +1,18 @@
+# Template file for 'bcftools'
+pkgname=bcftools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--with-htslib=system --enable-perl-filters --enable-libgsl"
+makedepends="htslib-devel zlib-devel gsl-devel perl"
+short_desc="Read/write BCF2/VCF/gVCF files and call/filter/sum SNP and short indels"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/bcftools/releases/download/${version}/bcftools-${version}.tar.bz2"
+checksum=13bfa1da2a5edda8fa51196a47a0b4afb3fef17516451e4f0e78477f3dd30b90
+python_version=3
+
+post_install() {
+	vlicense LICENSE
+}

From 4e28e07cef3235ebc15d4221cd2dc10d66c3971f Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 15:06:01 +0400
Subject: [PATCH 3/3] New package: samtools-1.13

---
 srcpkgs/samtools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/samtools/template

diff --git a/srcpkgs/samtools/template b/srcpkgs/samtools/template
new file mode 100644
index 000000000000..0d2ebb6f39f2
--- /dev/null
+++ b/srcpkgs/samtools/template
@@ -0,0 +1,18 @@
+# Template file for 'samtools'
+pkgname=samtools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--with-htslib=system"
+makedepends="htslib-devel zlib-devel ncurses-devel"
+checkdepends="perl"
+short_desc="Read/write/edit/index/view SAM/BAM/CRAM files"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/samtools/releases/download/${version}/samtools-${version}.tar.bz2"
+checksum=616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60
+
+post_install() {
+	vlicense LICENSE
+}

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

[zzaba]

[-- 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: 4348 bytes --]

From 9ecc5c74ec830cfe4498f8be2f151f6fdc43945e Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 15:05:37 +0400
Subject: [PATCH 1/3] New package: htslib-1.13

---
 common/shlibs           |  1 +
 srcpkgs/htslib-devel    |  1 +
 srcpkgs/htslib/template | 29 +++++++++++++++++++++++++++++
 3 files changed, 31 insertions(+)
 create mode 120000 srcpkgs/htslib-devel
 create mode 100644 srcpkgs/htslib/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/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..9a3b1413caf7
--- /dev/null
+++ b/srcpkgs/htslib/template
@@ -0,0 +1,29 @@
+# Template file for 'htslib'
+pkgname=htslib
+version=1.13
+revision=1
+build_style=gnu-configure
+makedepends="zlib-devel bzip2-devel liblzma-devel libcurl-devel openssl-devel"
+checkdepends="perl"
+short_desc="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/htslib/releases/download/${version}/htslib-${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
+	}
+}

From 91dfc704864b481a992c5801f3381974da938aa4 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 20:15:18 +0400
Subject: [PATCH 2/3] New package: bcftools-1.13

---
 srcpkgs/bcftools/template | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 srcpkgs/bcftools/template

diff --git a/srcpkgs/bcftools/template b/srcpkgs/bcftools/template
new file mode 100644
index 000000000000..17df809bcc4a
--- /dev/null
+++ b/srcpkgs/bcftools/template
@@ -0,0 +1,19 @@
+# Template file for 'bcftools'
+pkgname=bcftools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--with-htslib=system --enable-libgsl --enable-perl-filters"
+hostmakedepends="perl"
+makedepends="htslib-devel zlib-devel gsl-devel perl"
+short_desc="Read/write BCF2/VCF/gVCF files and call/filter/sum SNP and short indels"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/bcftools/releases/download/${version}/bcftools-${version}.tar.bz2"
+checksum=13bfa1da2a5edda8fa51196a47a0b4afb3fef17516451e4f0e78477f3dd30b90
+python_version=3
+
+post_install() {
+	vlicense LICENSE
+}

From f767c624511ae74916b8cb759534ee7b941f447f Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 20:15:22 +0400
Subject: [PATCH 3/3] New package: samtools-1.13

---
 srcpkgs/samtools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/samtools/template

diff --git a/srcpkgs/samtools/template b/srcpkgs/samtools/template
new file mode 100644
index 000000000000..0d2ebb6f39f2
--- /dev/null
+++ b/srcpkgs/samtools/template
@@ -0,0 +1,18 @@
+# Template file for 'samtools'
+pkgname=samtools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--with-htslib=system"
+makedepends="htslib-devel zlib-devel ncurses-devel"
+checkdepends="perl"
+short_desc="Read/write/edit/index/view SAM/BAM/CRAM files"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/samtools/releases/download/${version}/samtools-${version}.tar.bz2"
+checksum=616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60
+
+post_install() {
+	vlicense LICENSE
+}

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

[zzaba]

[-- 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

<!--
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build is likely to take several hours), make sure to
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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
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#### 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: 4348 bytes --]

From 9ecc5c74ec830cfe4498f8be2f151f6fdc43945e Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 15:05:37 +0400
Subject: [PATCH 1/3] New package: htslib-1.13

---
 common/shlibs           |  1 +
 srcpkgs/htslib-devel    |  1 +
 srcpkgs/htslib/template | 29 +++++++++++++++++++++++++++++
 3 files changed, 31 insertions(+)
 create mode 120000 srcpkgs/htslib-devel
 create mode 100644 srcpkgs/htslib/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/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..9a3b1413caf7
--- /dev/null
+++ b/srcpkgs/htslib/template
@@ -0,0 +1,29 @@
+# Template file for 'htslib'
+pkgname=htslib
+version=1.13
+revision=1
+build_style=gnu-configure
+makedepends="zlib-devel bzip2-devel liblzma-devel libcurl-devel openssl-devel"
+checkdepends="perl"
+short_desc="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/htslib/releases/download/${version}/htslib-${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
+	}
+}

From 91dfc704864b481a992c5801f3381974da938aa4 Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 20:15:18 +0400
Subject: [PATCH 2/3] New package: bcftools-1.13

---
 srcpkgs/bcftools/template | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 srcpkgs/bcftools/template

diff --git a/srcpkgs/bcftools/template b/srcpkgs/bcftools/template
new file mode 100644
index 000000000000..17df809bcc4a
--- /dev/null
+++ b/srcpkgs/bcftools/template
@@ -0,0 +1,19 @@
+# Template file for 'bcftools'
+pkgname=bcftools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--with-htslib=system --enable-libgsl --enable-perl-filters"
+hostmakedepends="perl"
+makedepends="htslib-devel zlib-devel gsl-devel perl"
+short_desc="Read/write BCF2/VCF/gVCF files and call/filter/sum SNP and short indels"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/bcftools/releases/download/${version}/bcftools-${version}.tar.bz2"
+checksum=13bfa1da2a5edda8fa51196a47a0b4afb3fef17516451e4f0e78477f3dd30b90
+python_version=3
+
+post_install() {
+	vlicense LICENSE
+}

From f767c624511ae74916b8cb759534ee7b941f447f Mon Sep 17 00:00:00 2001
From: Saba Gogichaishvili <sd.gogich@gmail.com>
Date: Wed, 11 Aug 2021 20:15:22 +0400
Subject: [PATCH 3/3] New package: samtools-1.13

---
 srcpkgs/samtools/template | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 srcpkgs/samtools/template

diff --git a/srcpkgs/samtools/template b/srcpkgs/samtools/template
new file mode 100644
index 000000000000..0d2ebb6f39f2
--- /dev/null
+++ b/srcpkgs/samtools/template
@@ -0,0 +1,18 @@
+# Template file for 'samtools'
+pkgname=samtools
+version=1.13
+revision=1
+build_style=gnu-configure
+configure_args="--with-htslib=system"
+makedepends="htslib-devel zlib-devel ncurses-devel"
+checkdepends="perl"
+short_desc="Read/write/edit/index/view SAM/BAM/CRAM files"
+maintainer="Saba Gogichaishvili <sd.gogich@gmail.com>"
+license="MIT"
+homepage="https://www.htslib.org/"
+distfiles="https://github.com/samtools/samtools/releases/download/${version}/samtools-${version}.tar.bz2"
+checksum=616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60
+
+post_install() {
+	vlicense LICENSE
+}

Re: New package: samtools-1.13

[github-actions]

[-- Attachment #1: Type: text/plain, Size: 305 bytes --]

New comment by github-actions[bot] on void-packages repository

https://github.com/void-linux/void-packages/pull/32419#issuecomment-1143044637

Comment:
Pull Requests become stale 90 days after last activity and are closed 14 days after that.  If this pull request is still relevant bump it or assign it.

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

[github-actions]

[-- Attachment #1: Type: text/plain, Size: 1335 bytes --]

There's a closed pull request on the void-packages repository

New package: samtools-1.13
https://github.com/void-linux/void-packages/pull/32419

Description:
<!-- 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