[bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools

[Roel Janssen <roel@gnu.org>]

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Hi Guix,

The following patches update htslib, bcftools, samtools, and bedtools.
I've succesfully built bedtools with the latest samtools instead of the
1.9 version.

Kind regards,
Roel Janssen


[-- Attachment #2: 0004-gnu-Update-bedtools-to-2.30.0.patch --]
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From 4549f622042cb8c04165d85ff922d129f7c10553 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 16 Apr 2021 11:52:16 +0200
Subject: [PATCH 4/4] gnu: Update bedtools to 2.30.0.

* gnu/packages/bioinformatics.scm (bedtools): Update to 2.30.0,
  [inputs]: Use latest samtools.
---
 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 2a20971089..94bf917df5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -453,7 +453,7 @@ computational cluster.")
 (define-public bedtools
   (package
     (name "bedtools")
-    (version "2.29.2")
+    (version "2.30.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/arq5x/bedtools2/releases/"
@@ -461,7 +461,7 @@ computational cluster.")
                                   "bedtools-" version ".tar.gz"))
               (sha256
                (base32
-                "0m3hk6548846w83a9s5drsczvy67n2azx41kj71n03klb2gbzwg3"))))
+                "1f2hh79l7dn147c2xyfgf5wfjvlqfw32kjfnnh2n1qy6rpzx2fik"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"
@@ -473,7 +473,7 @@ computational cluster.")
     (native-inputs
      `(("python" ,python-wrapper)))
     (inputs
-     `(("samtools" ,samtools-1.9)
+     `(("samtools" ,samtools)
        ("zlib" ,zlib)))
     (home-page "https://github.com/arq5x/bedtools2")
     (synopsis "Tools for genome analysis and arithmetic")
-- 
2.30.2


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From 6a18bd05cdd181b19ab99f92f1ef87f1554c622d Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 16 Apr 2021 11:51:41 +0200
Subject: [PATCH 3/4] gnu: Update samtools to 1.12.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.12.
---
 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 a7cffdf83c..2a20971089 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5901,7 +5901,7 @@ to the user's query of interest.")
 (define-public samtools
   (package
     (name "samtools")
-    (version "1.11")
+    (version "1.12")
     (source
      (origin
        (method url-fetch)
@@ -5910,11 +5910,11 @@ to the user's query of interest.")
                        version "/samtools-" version ".tar.bz2"))
        (sha256
         (base32
-         "1dp5wknak4arnw5ghhif9mmljlfnw5bgm91wib7z0j8wdjywx0z2"))
+         "1jrdj2idpma5ja9cg0rr73b565vdbr9wyy6zig54bidicc2pg8vd"))
        (modules '((guix build utils)))
        (snippet '(begin
                    ;; Delete bundled htslib.
-                   (delete-file-recursively "htslib-1.11")
+                   (delete-file-recursively "htslib-1.12")
                    #t))))
     (build-system gnu-build-system)
     (arguments
-- 
2.30.2


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From f1513d7b43fa14e15d945c92fb9fa2c6451a46b9 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 16 Apr 2021 11:50:53 +0200
Subject: [PATCH 2/4] gnu: Update bcftools to 1.12.

* gnu/packages/bioinformatics.scm (bcftools): Update to 1.12.
---
 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 e385e07cea..a7cffdf83c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -327,7 +327,7 @@ BAM files.")
 (define-public bcftools
   (package
     (name "bcftools")
-    (version "1.11")
+    (version "1.12")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/samtools/bcftools/"
@@ -335,11 +335,11 @@ BAM files.")
                                   version "/bcftools-" version ".tar.bz2"))
               (sha256
                (base32
-                "0r508mp15pqzf8r1269kb4v5naw9zsvbwd3cz8s1yj7carsf9viw"))
+                "1x94l1hy2pi3lbz0sxlbw0g6q5z5apcrhrlcwda94ns9n4r6a3ks"))
               (modules '((guix build utils)))
               (snippet '(begin
                           ;; Delete bundled htslib.
-                          (delete-file-recursively "htslib-1.11")
+                          (delete-file-recursively "htslib-1.12")
                           #t))))
     (build-system gnu-build-system)
     (arguments
-- 
2.30.2


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From 45e578976cd0c77e60d2188385adcda51b23b92a Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 16 Apr 2021 11:49:49 +0200
Subject: [PATCH 1/4] gnu: htslib: Update to 1.12.

* gnu/packages/bioinformatics.scm (htslib): Update to 1.12.
---
 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 41ef4cd513..e385e07cea 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4476,7 +4476,7 @@ performance.")
 (define-public htslib
   (package
     (name "htslib")
-    (version "1.11")
+    (version "1.12")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -4484,7 +4484,7 @@ performance.")
                     version "/htslib-" version ".tar.bz2"))
               (sha256
                (base32
-                "1mrq4mihzx37yqhj3sfz6da6mw49niia808bzsw2gkkgmadxvyng"))))
+                "1jplnvizgr0fyyvvmkfmnsywrrpqhid3760vw15bllz98qdi9012"))))
     (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
-- 
2.30.2