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

From: Roel Janssen <[email-masked]>
Date: Fri, 16 Apr 2021 11:55:39 +0200

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

From 4549f622042cb8c04165d85ff922d129f7c10553 Mon Sep 17 00:00:00 2001
From: Roel Janssen <[email-masked]>
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

From 6a18bd05cdd181b19ab99f92f1ef87f1554c622d Mon Sep 17 00:00:00 2001
From: Roel Janssen <[email-masked]>
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

From f1513d7b43fa14e15d945c92fb9fa2c6451a46b9 Mon Sep 17 00:00:00 2001
From: Roel Janssen <[email-masked]>
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

From 45e578976cd0c77e60d2188385adcda51b23b92a Mon Sep 17 00:00:00 2001
From: Roel Janssen <[email-masked]>
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