[bug#44304] [PATCH] gnu: Update htslib to 1.11.

[bug#44304] [PATCH] gnu: Update htslib to 1.11.

[Roel Janssen]

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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 --]
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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

[bug#44304] [PATCH] gnu: Update htslib to 1.11.

[Roel Janssen]

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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



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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


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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

[bug#44304] [PATCH] gnu: Update htslib to 1.11.

[Ricardo Wurmus]

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

[bug#44304] [PATCH] gnu: Update htslib to 1.11.

[Roel Janssen]

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