[PATCH] gnu: Update htslib to 1.11.

  • Done
  • quality assurance status badge
Details
2 participants
  • Ricardo Wurmus
  • Roel Janssen
Owner
unassigned
Submitted by
Roel Janssen
Severity
normal
R
R
Roel Janssen wrote on 29 Oct 2020 11:44
(address . guix-patches@gnu.org)
6ccd23fc29b49611b82d9cc26461dfc294796aa3.camel@gnu.org
Dear Guix,

I'd like to update htslib to 1.11. The patch is straightfoward.

Kind regards,
Roel Janssen
From 8ed33ee9ce51e7e64faf5f3aad0684eb965ed131 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 29 Oct 2020 11:41:27 +0100
Subject: [PATCH] gnu: Update htslib to 1.11.

* gnu/packages/bioinformatics.scm (htslib): Update to 1.11.
---
gnu/packages/bioinformatics.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (24 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 41d92401ad..09216f6a8d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4215,7 +4215,7 @@ performance.")
(define-public htslib
(package
(name "htslib")
- (version "1.9")
+ (version "1.11")
(source (origin
(method url-fetch)
(uri (string-append
@@ -4223,7 +4223,7 @@ performance.")
version "/htslib-" version ".tar.bz2"))
(sha256
(base32
- "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0"))))
+ "1mrq4mihzx37yqhj3sfz6da6mw49niia808bzsw2gkkgmadxvyng"))))
(build-system gnu-build-system)
;; Let htslib translate "gs://" and "s3://" to regular https links with
;; "--enable-gcs" and "--enable-s3". For these options to work, we also
--
2.26.2
R
R
Roel Janssen wrote on 29 Oct 2020 12:01
(address . guix-patches@gnu.org)(address . 44304@debbugs.gnu.org)
08b421af5c82326cae13054e014e926b6b3c4ece.camel@gnu.org
On Thu, 2020-10-29 at 11:44 +0100, Roel Janssen wrote:
Toggle quote (7 lines)
> Dear Guix,
>
> I'd like to update htslib to 1.11.  The patch is straightfoward.
>
> Kind regards,
> Roel Janssen

In addition to htslib, it'd be good to keep samtools and bcftools in
sync. So here are the patches for bcftools and samtools.

Kind regards,
Roel Janssen
From 4025b622017f6ff0f365bf827c0f4bf06603f9ed Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 29 Oct 2020 11:58:02 +0100
Subject: [PATCH 3/3] gnu: Update samtools to 1.11.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.11.
---
gnu/packages/bioinformatics.scm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)

Toggle diff (29 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a428ba1fed..4c49b00252 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5613,7 +5613,7 @@ to the user's query of interest.")
(define-public samtools
(package
(name "samtools")
- (version "1.9")
+ (version "1.11")
(source
(origin
(method url-fetch)
@@ -5622,11 +5622,11 @@ to the user's query of interest.")
version "/samtools-" version ".tar.bz2"))
(sha256
(base32
- "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8"))
+ "1dp5wknak4arnw5ghhif9mmljlfnw5bgm91wib7z0j8wdjywx0z2"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
- (delete-file-recursively "htslib-1.9")
+ (delete-file-recursively "htslib-1.11")
#t))))
(build-system gnu-build-system)
(arguments
--
2.26.2
From 20a16449cd640f32798cb36f942eb44faaa9f661 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 29 Oct 2020 11:57:16 +0100
Subject: [PATCH 2/3] gnu: Update bcftools to 1.11.

* gnu/packages/bioinformatics.scm (bcftools): Update to 1.11.
---
gnu/packages/bioinformatics.scm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)

Toggle diff (29 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 09216f6a8d..a428ba1fed 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -313,7 +313,7 @@ BAM files.")
(define-public bcftools
(package
(name "bcftools")
- (version "1.9")
+ (version "1.11")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/samtools/bcftools/"
@@ -321,11 +321,11 @@ BAM files.")
version "/bcftools-" version ".tar.bz2"))
(sha256
(base32
- "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg"))
+ "0r508mp15pqzf8r1269kb4v5naw9zsvbwd3cz8s1yj7carsf9viw"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
- (delete-file-recursively "htslib-1.9")
+ (delete-file-recursively "htslib-1.11")
#t))))
(build-system gnu-build-system)
(arguments
--
2.26.2
R
R
Ricardo Wurmus wrote on 29 Oct 2020 13:55
Re: [bug#44304] [PATCH] gnu: Update htslib to 1.11.
(name . Roel Janssen)(address . roel@gnu.org)
877dr9199t.fsf@elephly.net
Roel Janssen <roel@gnu.org> writes:

Toggle quote (11 lines)
> On Thu, 2020-10-29 at 11:44 +0100, Roel Janssen wrote:
>> Dear Guix,
>>
>> I'd like to update htslib to 1.11. The patch is straightfoward.
>>
>> Kind regards,
>> Roel Janssen
>
> In addition to htslib, it'd be good to keep samtools and bcftools in
> sync. So here are the patches for bcftools and samtools.

These patches look good to me!

--
Ricardo
R
R
Roel Janssen wrote on 29 Oct 2020 16:56
(name . Ricardo Wurmus)(address . rekado@elephly.net)
350a7d938aaca3d7379b9ef746d3d92064553b5a.camel@gnu.org
On Thu, 2020-10-29 at 13:55 +0100, Ricardo Wurmus wrote:
Toggle quote (18 lines)
>
> Roel Janssen <roel@gnu.org> writes:
>
> > On Thu, 2020-10-29 at 11:44 +0100, Roel Janssen wrote:
> > > Dear Guix,
> > >
> > > I'd like to update htslib to 1.11.  The patch is straightfoward.
> > >
> > > Kind regards,
> > > Roel Janssen
> >
> > In addition to htslib, it'd be good to keep samtools and bcftools
> > in
> > sync.  So here are the patches for bcftools and samtools.
>
> These patches look good to me!
>

Thank you for the quick review! I pushed them in
bcbd536e3f22e7bcce6ef535171f4257c79d2f0c,
04a49b414303c329032f74de67541cc39d2271c6, and
f40add4dbb45a5a87fd5213e23e7ab0cc77c008e.

Kind regards,
Roel Janssen
?