* [bug#44304] [PATCH] gnu: Update htslib to 1.11.
@ 2020-10-29 10:44 Roel Janssen
2020-10-29 11:01 ` Roel Janssen
0 siblings, 1 reply; 4+ messages in thread
From: Roel Janssen @ 2020-10-29 10:44 UTC (permalink / raw)
To: 44304
[-- Attachment #1: Type: text/plain, Size: 105 bytes --]
Dear Guix,
I'd like to update htslib to 1.11. The patch is straightfoward.
Kind regards,
Roel Janssen
[-- Attachment #2: 0001-gnu-Update-htslib-to-1.11.patch --]
[-- Type: text/x-patch, Size: 1262 bytes --]
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(-)
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
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#44304] [PATCH] gnu: Update htslib to 1.11.
2020-10-29 10:44 [bug#44304] [PATCH] gnu: Update htslib to 1.11 Roel Janssen
@ 2020-10-29 11:01 ` Roel Janssen
2020-10-29 12:55 ` Ricardo Wurmus
0 siblings, 1 reply; 4+ messages in thread
From: Roel Janssen @ 2020-10-29 11:01 UTC (permalink / raw)
To: 44304
[-- Attachment #1: Type: text/plain, Size: 331 bytes --]
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.
Kind regards,
Roel Janssen
[-- Attachment #2: 0003-gnu-Update-samtools-to-1.11.patch --]
[-- Type: text/x-patch, Size: 1374 bytes --]
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(-)
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
[-- Attachment #3: 0002-gnu-Update-bcftools-to-1.11.patch --]
[-- Type: text/x-patch, Size: 1483 bytes --]
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(-)
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
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#44304] [PATCH] gnu: Update htslib to 1.11.
2020-10-29 11:01 ` Roel Janssen
@ 2020-10-29 12:55 ` Ricardo Wurmus
2020-10-29 15:56 ` Roel Janssen
0 siblings, 1 reply; 4+ messages in thread
From: Ricardo Wurmus @ 2020-10-29 12:55 UTC (permalink / raw)
To: Roel Janssen; +Cc: 44304
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!
--
Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
* [bug#44304] [PATCH] gnu: Update htslib to 1.11.
2020-10-29 12:55 ` Ricardo Wurmus
@ 2020-10-29 15:56 ` Roel Janssen
0 siblings, 0 replies; 4+ messages in thread
From: Roel Janssen @ 2020-10-29 15:56 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: 44304-done, 44304
On Thu, 2020-10-29 at 13:55 +0100, Ricardo Wurmus wrote:
>
> 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
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2020-10-29 15:57 UTC | newest]
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2020-10-29 10:44 [bug#44304] [PATCH] gnu: Update htslib to 1.11 Roel Janssen
2020-10-29 11:01 ` Roel Janssen
2020-10-29 12:55 ` Ricardo Wurmus
2020-10-29 15:56 ` Roel Janssen
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