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* [PR PATCH] New package: samtools-1.13
@ 2021-08-08 22:29 zzaba
  2021-08-08 23:04 ` [PR PATCH] [Updated] " zzaba
                   ` (35 more replies)
  0 siblings, 36 replies; 37+ messages in thread
From: zzaba @ 2021-08-08 22:29 UTC (permalink / raw)
  To: ml

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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? 
(Please choose at least one native build and, if supported, at least one cross build. More are better.)
- [ ] 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
  - [ ] armv7l
  - [ ] armv6l-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
+}

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR PATCH] [Updated] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
@ 2021-08-08 23:04 ` zzaba
  2021-08-08 23:10 ` zzaba
                   ` (34 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-08 23:04 UTC (permalink / raw)
  To: ml

[-- 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: 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
+}

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR PATCH] [Updated] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
  2021-08-08 23:04 ` [PR PATCH] [Updated] " zzaba
@ 2021-08-08 23:10 ` zzaba
  2021-08-09 13:11 ` jmarshall
                   ` (33 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-08 23:10 UTC (permalink / raw)
  To: ml

[-- 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: 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
+}

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
  2021-08-08 23:04 ` [PR PATCH] [Updated] " zzaba
  2021-08-08 23:10 ` zzaba
@ 2021-08-09 13:11 ` jmarshall
  2021-08-09 16:18 ` zzaba
                   ` (32 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: jmarshall @ 2021-08-09 13:11 UTC (permalink / raw)
  To: ml

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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?

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (2 preceding siblings ...)
  2021-08-09 13:11 ` jmarshall
@ 2021-08-09 16:18 ` zzaba
  2021-08-09 16:26 ` zzaba
                   ` (31 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-09 16:18 UTC (permalink / raw)
  To: ml

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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.

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (3 preceding siblings ...)
  2021-08-09 16:18 ` zzaba
@ 2021-08-09 16:26 ` zzaba
  2021-08-09 17:04 ` paper42
                   ` (30 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-09 16:26 UTC (permalink / raw)
  To: ml

[-- 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. 

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (4 preceding siblings ...)
  2021-08-09 16:26 ` zzaba
@ 2021-08-09 17:04 ` paper42
  2021-08-09 17:05 ` zzaba
                   ` (29 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: paper42 @ 2021-08-09 17:04 UTC (permalink / raw)
  To: ml

[-- Attachment #1: Type: text/plain, Size: 492 bytes --]

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

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (5 preceding siblings ...)
  2021-08-09 17:04 ` paper42
@ 2021-08-09 17:05 ` zzaba
  2021-08-09 17:22 ` paper42
                   ` (28 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-09 17:05 UTC (permalink / raw)
  To: ml

[-- 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?

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (6 preceding siblings ...)
  2021-08-09 17:05 ` zzaba
@ 2021-08-09 17:22 ` paper42
  2021-08-09 21:16 ` [PR PATCH] [Updated] " zzaba
                   ` (27 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: paper42 @ 2021-08-09 17:22 UTC (permalink / raw)
  To: ml

[-- 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.

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR PATCH] [Updated] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (7 preceding siblings ...)
  2021-08-09 17:22 ` paper42
@ 2021-08-09 21:16 ` zzaba
  2021-08-09 21:17 ` abenson
                   ` (26 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-09 21:16 UTC (permalink / raw)
  To: ml

[-- 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
+}

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (8 preceding siblings ...)
  2021-08-09 21:16 ` [PR PATCH] [Updated] " zzaba
@ 2021-08-09 21:17 ` abenson
  2021-08-09 21:20 ` zzaba
                   ` (25 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: abenson @ 2021-08-09 21:17 UTC (permalink / raw)
  To: ml

[-- 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.

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (9 preceding siblings ...)
  2021-08-09 21:17 ` abenson
@ 2021-08-09 21:20 ` zzaba
  2021-08-09 21:23 ` paper42
                   ` (24 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-09 21:20 UTC (permalink / raw)
  To: ml

[-- 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

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (10 preceding siblings ...)
  2021-08-09 21:20 ` zzaba
@ 2021-08-09 21:23 ` paper42
  2021-08-09 21:28 ` [PR PATCH] [Updated] " zzaba
                   ` (23 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: paper42 @ 2021-08-09 21:23 UTC (permalink / raw)
  To: ml

[-- 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

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR PATCH] [Updated] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (11 preceding siblings ...)
  2021-08-09 21:23 ` paper42
@ 2021-08-09 21:28 ` zzaba
  2021-08-09 21:41 ` zzaba
                   ` (22 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-09 21:28 UTC (permalink / raw)
  To: ml

[-- 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

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR PATCH] [Updated] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (12 preceding siblings ...)
  2021-08-09 21:28 ` [PR PATCH] [Updated] " zzaba
@ 2021-08-09 21:41 ` zzaba
  2021-08-09 22:19 ` zzaba
                   ` (21 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-09 21:41 UTC (permalink / raw)
  To: ml

[-- 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
+	}
+}

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR PATCH] [Updated] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (13 preceding siblings ...)
  2021-08-09 21:41 ` zzaba
@ 2021-08-09 22:19 ` zzaba
  2021-08-09 22:44 ` zzaba
                   ` (20 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-09 22:19 UTC (permalink / raw)
  To: ml

[-- 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
+	}
+}

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR PATCH] [Updated] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (14 preceding siblings ...)
  2021-08-09 22:19 ` zzaba
@ 2021-08-09 22:44 ` zzaba
  2021-08-10 18:33 ` [PR REVIEW] " ericonr
                   ` (19 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-09 22:44 UTC (permalink / raw)
  To: ml

[-- 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
+	}
+}

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (15 preceding siblings ...)
  2021-08-09 22:44 ` zzaba
@ 2021-08-10 18:33 ` ericonr
  2021-08-10 18:33 ` ericonr
                   ` (18 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: ericonr @ 2021-08-10 18:33 UTC (permalink / raw)
  To: ml

[-- 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.

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (16 preceding siblings ...)
  2021-08-10 18:33 ` [PR REVIEW] " ericonr
@ 2021-08-10 18:33 ` ericonr
  2021-08-10 18:33 ` ericonr
                   ` (17 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: ericonr @ 2021-08-10 18:33 UTC (permalink / raw)
  To: ml

[-- 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"

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (17 preceding siblings ...)
  2021-08-10 18:33 ` ericonr
@ 2021-08-10 18:33 ` ericonr
  2021-08-10 18:33 ` ericonr
                   ` (16 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: ericonr @ 2021-08-10 18:33 UTC (permalink / raw)
  To: ml

[-- 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.

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (18 preceding siblings ...)
  2021-08-10 18:33 ` ericonr
@ 2021-08-10 18:33 ` ericonr
  2021-08-10 19:59 ` zzaba
                   ` (15 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: ericonr @ 2021-08-10 18:33 UTC (permalink / raw)
  To: ml

[-- 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"

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (19 preceding siblings ...)
  2021-08-10 18:33 ` ericonr
@ 2021-08-10 19:59 ` zzaba
  2021-08-10 20:00 ` zzaba
                   ` (14 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-10 19:59 UTC (permalink / raw)
  To: ml

[-- 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).

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (20 preceding siblings ...)
  2021-08-10 19:59 ` zzaba
@ 2021-08-10 20:00 ` zzaba
  2021-08-10 20:38 ` paper42
                   ` (13 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-10 20:00 UTC (permalink / raw)
  To: ml

[-- 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?

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (21 preceding siblings ...)
  2021-08-10 20:00 ` zzaba
@ 2021-08-10 20:38 ` paper42
  2021-08-10 20:45 ` zzaba
                   ` (12 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: paper42 @ 2021-08-10 20:38 UTC (permalink / raw)
  To: ml

[-- 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

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (22 preceding siblings ...)
  2021-08-10 20:38 ` paper42
@ 2021-08-10 20:45 ` zzaba
  2021-08-10 20:59 ` paper42
                   ` (11 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-10 20:45 UTC (permalink / raw)
  To: ml

[-- 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?

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (23 preceding siblings ...)
  2021-08-10 20:45 ` zzaba
@ 2021-08-10 20:59 ` paper42
  2021-08-10 21:03 ` [PR PATCH] [Updated] " zzaba
                   ` (10 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: paper42 @ 2021-08-10 20:59 UTC (permalink / raw)
  To: ml

[-- 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.

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR PATCH] [Updated] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (24 preceding siblings ...)
  2021-08-10 20:59 ` paper42
@ 2021-08-10 21:03 ` zzaba
  2021-08-11  2:03 ` [PR REVIEW] " ericonr
                   ` (9 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-10 21:03 UTC (permalink / raw)
  To: ml

[-- 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
+}

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (25 preceding siblings ...)
  2021-08-10 21:03 ` [PR PATCH] [Updated] " zzaba
@ 2021-08-11  2:03 ` ericonr
  2021-08-11  8:50 ` jmarshall
                   ` (8 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: ericonr @ 2021-08-11  2:03 UTC (permalink / raw)
  To: ml

[-- 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?

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (26 preceding siblings ...)
  2021-08-11  2:03 ` [PR REVIEW] " ericonr
@ 2021-08-11  8:50 ` jmarshall
  2021-08-11  9:27 ` jmarshall
                   ` (7 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: jmarshall @ 2021-08-11  8:50 UTC (permalink / raw)
  To: ml

[-- 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`.

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (27 preceding siblings ...)
  2021-08-11  8:50 ` jmarshall
@ 2021-08-11  9:27 ` jmarshall
  2021-08-11 10:56 ` zzaba
                   ` (6 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: jmarshall @ 2021-08-11  9:27 UTC (permalink / raw)
  To: ml

[-- 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`.

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (28 preceding siblings ...)
  2021-08-11  9:27 ` jmarshall
@ 2021-08-11 10:56 ` zzaba
  2021-08-11 10:57 ` zzaba
                   ` (5 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-11 10:56 UTC (permalink / raw)
  To: ml

[-- 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.

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR REVIEW] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (29 preceding siblings ...)
  2021-08-11 10:56 ` zzaba
@ 2021-08-11 10:57 ` zzaba
  2021-08-11 11:11 ` [PR PATCH] [Updated] " zzaba
                   ` (4 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-11 10:57 UTC (permalink / raw)
  To: ml

[-- 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

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR PATCH] [Updated] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (30 preceding siblings ...)
  2021-08-11 10:57 ` zzaba
@ 2021-08-11 11:11 ` zzaba
  2021-08-11 16:16 ` zzaba
                   ` (3 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-11 11:11 UTC (permalink / raw)
  To: ml

[-- 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
+}

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR PATCH] [Updated] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (31 preceding siblings ...)
  2021-08-11 11:11 ` [PR PATCH] [Updated] " zzaba
@ 2021-08-11 16:16 ` zzaba
  2021-08-13 20:44 ` zzaba
                   ` (2 subsequent siblings)
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-11 16:16 UTC (permalink / raw)
  To: ml

[-- 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
+}

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR PATCH] [Updated] New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (32 preceding siblings ...)
  2021-08-11 16:16 ` zzaba
@ 2021-08-13 20:44 ` zzaba
  2022-06-01  2:15 ` github-actions
  2022-06-15  2:16 ` [PR PATCH] [Closed]: " github-actions
  35 siblings, 0 replies; 37+ messages in thread
From: zzaba @ 2021-08-13 20:44 UTC (permalink / raw)
  To: ml

[-- 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
+}

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (33 preceding siblings ...)
  2021-08-13 20:44 ` zzaba
@ 2022-06-01  2:15 ` github-actions
  2022-06-15  2:16 ` [PR PATCH] [Closed]: " github-actions
  35 siblings, 0 replies; 37+ messages in thread
From: github-actions @ 2022-06-01  2:15 UTC (permalink / raw)
  To: ml

[-- 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.

^ permalink raw reply	[flat|nested] 37+ messages in thread

* Re: [PR PATCH] [Closed]: New package: samtools-1.13
  2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
                   ` (34 preceding siblings ...)
  2022-06-01  2:15 ` github-actions
@ 2022-06-15  2:16 ` github-actions
  35 siblings, 0 replies; 37+ messages in thread
From: github-actions @ 2022-06-15  2:16 UTC (permalink / raw)
  To: ml

[-- 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).
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acceptable to skip CI.
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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


^ permalink raw reply	[flat|nested] 37+ messages in thread

end of thread, other threads:[~2022-06-15  2:16 UTC | newest]

Thread overview: 37+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2021-08-08 22:29 [PR PATCH] New package: samtools-1.13 zzaba
2021-08-08 23:04 ` [PR PATCH] [Updated] " zzaba
2021-08-08 23:10 ` zzaba
2021-08-09 13:11 ` jmarshall
2021-08-09 16:18 ` zzaba
2021-08-09 16:26 ` zzaba
2021-08-09 17:04 ` paper42
2021-08-09 17:05 ` zzaba
2021-08-09 17:22 ` paper42
2021-08-09 21:16 ` [PR PATCH] [Updated] " zzaba
2021-08-09 21:17 ` abenson
2021-08-09 21:20 ` zzaba
2021-08-09 21:23 ` paper42
2021-08-09 21:28 ` [PR PATCH] [Updated] " zzaba
2021-08-09 21:41 ` zzaba
2021-08-09 22:19 ` zzaba
2021-08-09 22:44 ` zzaba
2021-08-10 18:33 ` [PR REVIEW] " ericonr
2021-08-10 18:33 ` ericonr
2021-08-10 18:33 ` ericonr
2021-08-10 18:33 ` ericonr
2021-08-10 19:59 ` zzaba
2021-08-10 20:00 ` zzaba
2021-08-10 20:38 ` paper42
2021-08-10 20:45 ` zzaba
2021-08-10 20:59 ` paper42
2021-08-10 21:03 ` [PR PATCH] [Updated] " zzaba
2021-08-11  2:03 ` [PR REVIEW] " ericonr
2021-08-11  8:50 ` jmarshall
2021-08-11  9:27 ` jmarshall
2021-08-11 10:56 ` zzaba
2021-08-11 10:57 ` zzaba
2021-08-11 11:11 ` [PR PATCH] [Updated] " zzaba
2021-08-11 16:16 ` zzaba
2021-08-13 20:44 ` zzaba
2022-06-01  2:15 ` github-actions
2022-06-15  2:16 ` [PR PATCH] [Closed]: " github-actions

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