From: Roel Janssen <roel@gnu.org>
To: 44613@debbugs.gnu.org
Subject: [bug#44613] [PATCH] Fix build for bedtools
Date: Fri, 13 Nov 2020 12:01:04 +0100 [thread overview]
Message-ID: <a82f869c91b6b33a5d063b505cab01e19b53b84d.camel@gnu.org> (raw)
[-- Attachment #1: Type: text/plain, Size: 556 bytes --]
Dear Guix,
By updating samtools to 1.11, I introduced a build failure for
bedtools. More precisely, the tests for intersect break in precisely
this way:
https://github.com/arq5x/bedtools2/issues/814
With the following patches, I'd like to add samtools-1.9, htslib-1.9
(samtools depends on that) to fix this problem with bedtools.
Alternatively we could add a patch to disable the failing bedtools
tests. I manually inspected the test results, and seem to match
perfectly (indicating that there's no problem with bedtools).
Kind regards,
Roel Janssen
[-- Attachment #2: 0003-gnu-bedtools-Use-samtools-1.9.patch --]
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From 2541b3c44e695ff1a6b56128b6efa72c463c0b0a Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 13 Nov 2020 11:29:38 +0100
Subject: [PATCH 3/3] gnu: bedtools: Use samtools-1.9.
The build for bedtools with samtools 1.11 triggers a testsuite
failure which is reported here:
https://github.com/arq5x/bedtools2/issues/814
* gnu/packages/bioinformatics.scm (bedtools): Use samtools-1.9.
---
gnu/packages/bioinformatics.scm | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e047aebd1d..8ad38ac498 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -437,7 +437,7 @@ computational cluster.")
(native-inputs
`(("python" ,python-wrapper)))
(inputs
- `(("samtools" ,samtools)
+ `(("samtools" ,samtools-1.9)
("zlib" ,zlib)))
(home-page "https://github.com/arq5x/bedtools2")
(synopsis "Tools for genome analysis and arithmetic")
--
2.29.2
[-- Attachment #3: 0002-gnu-Add-samtools-1.9.patch --]
[-- Type: text/x-patch, Size: 1635 bytes --]
From 7881fd95bcddc0fee4717fab30dbb276745825d8 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 13 Nov 2020 11:29:20 +0100
Subject: [PATCH 2/3] gnu: Add samtools-1.9.
* gnu/packages/bioinformatics.scm (samtools-1.9): New variable.
---
gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ba86333fc3..e047aebd1d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5699,6 +5699,31 @@ variant calling (in conjunction with bcftools), and a simple alignment
viewer.")
(license license:expat)))
+(define-public samtools-1.9
+ (package (inherit samtools)
+ (name "samtools")
+ (version "1.9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append "mirror://sourceforge/samtools/samtools/"
+ version "/samtools-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8"))
+ (modules '((guix build utils)))
+ (snippet '(begin
+ ;; Delete bundled htslib.
+ (delete-file-recursively "htslib-1.9")
+ #t))))
+ (inputs
+ `(("htslib" ,htslib-1.9)
+ ("ncurses" ,ncurses)
+ ("perl" ,perl)
+ ("python" ,python)
+ ("zlib" ,zlib)))))
+
(define-public samtools-0.1
;; This is the most recent version of the 0.1 line of samtools. The input
;; and output formats differ greatly from that used and produced by samtools
--
2.29.2
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From 220604159383b09e11a7b0bed51237257c7c0442 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 13 Nov 2020 11:28:43 +0100
Subject: [PATCH 1/3] gnu: Add htslib-1.9.
* gnu/packages/bioinformatics.scm (htslib-1.9): New variable.
---
gnu/packages/bioinformatics.scm | 13 +++++++++++++
1 file changed, 13 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 06972dee51..ba86333fc3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4250,6 +4250,19 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and
;; the rest is released under the Expat license
(license (list license:expat license:bsd-3))))
+(define-public htslib-1.9
+ (package (inherit htslib)
+ (name "htslib")
+ (version "1.9")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/samtools/htslib/releases/download/"
+ version "/htslib-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0"))))))
+
;; This package should be removed once no packages rely upon it.
(define htslib-1.3
(package
--
2.29.2
next reply other threads:[~2020-11-13 11:02 UTC|newest]
Thread overview: 7+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-11-13 11:01 Roel Janssen [this message]
2020-11-13 12:39 ` [bug#44613] [PATCH] Fix build for bedtools zimoun
2020-11-13 12:55 ` Roel Janssen
2020-11-13 13:34 ` zimoun
2020-11-13 14:00 ` bug#44613: " Roel Janssen
2020-11-13 15:08 ` [bug#44613] " Marius Bakke
2020-11-13 15:51 ` [bug#44613] what “guix build -S” should return? zimoun
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