* [PATCH] Add CD-HIT
@ 2016-03-11 14:18 Ricardo Wurmus
2016-03-11 16:02 ` Ben Woodcroft
0 siblings, 1 reply; 5+ messages in thread
From: Ricardo Wurmus @ 2016-03-11 14:18 UTC (permalink / raw)
To: guix-devel
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: 0001-gnu-Add-CD-HIT.patch --]
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From 19d0402a90ee8f93f099fb026a7ba5436f77a21b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 11 Mar 2016 14:57:29 +0100
Subject: [PATCH] gnu: Add CD-HIT.
* gnu/packages/bioinformatics.scm (cd-hit): New variable.
---
gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 50 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5cb5fa2..2f0d2db 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -875,6 +875,56 @@ also includes an interface for tabix.")
(define-public python2-pysam
(package-with-python2 python-pysam))
+(define-public cd-hit
+ (package
+ (name "cd-hit")
+ (version "4.6.5")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/weizhongli/cdhit"
+ "/releases/download/V" version
+ "/cd-hit-v" version "-2016-0304.tar.gz"))
+ (sha256
+ (base32
+ "15db0hq38yyifwqx9b6l34z14jcq576dmjavhj8a426c18lvnhp3"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are no tests
+ #:make-flags
+ ;; Executables are copied directly to the PREFIX.
+ (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin"))
+ #:phases
+ (modify-phases %standard-phases
+ ;; No "configure" script
+ (delete 'configure)
+ ;; Remove sources of non-determinism
+ (add-after 'unpack 'be-timeless
+ (lambda _
+ (substitute* "cdhit-utility.c++"
+ ((" \\(built on \" __DATE__ \"\\)") ""))
+ (substitute* "cdhit-common.c++"
+ (("__DATE__") "\"0\"")
+ (("\", %s, \" __TIME__ \"\\\\n\", date") ""))
+ #t))
+ ;; The "install" target does not create the target directory
+ (add-before 'install 'create-target-dir
+ (lambda* (#:key outputs #:allow-other-keys)
+ (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
+ #t)))))
+ (inputs
+ `(("perl" ,perl)))
+ (home-page "http://weizhongli-lab.org/cd-hit/")
+ (synopsis "Cluster and compare protein or nucleotide sequences")
+ (description
+ "CD-HIT is a program for clustering and comparing protein or nucleotide
+sequences. CD-HIT is very fast and can handle extremely large databases.
+CD-HIT helps to significantly reduce the computational and manual efforts in
+many sequence analysis tasks and aids in understanding the data structure and
+correct the bias within a dataset.")
+ ;; The manual says: "It can be copied under the GNU General Public License
+ ;; version 2 (GPLv2)."
+ (license license:gpl2)))
+
(define-public clipper
(package
(name "clipper")
--
2.1.0
^ permalink raw reply related [flat|nested] 5+ messages in thread* Re: [PATCH] Add CD-HIT
2016-03-11 14:18 [PATCH] Add CD-HIT Ricardo Wurmus
@ 2016-03-11 16:02 ` Ben Woodcroft
0 siblings, 0 replies; 5+ messages in thread
From: Ben Woodcroft @ 2016-03-11 16:02 UTC (permalink / raw)
To: Ricardo Wurmus, guix-devel
Hi Ricardo,
Looks good, and much the same as the patch I hadn't got around to
submitting minus your good work with determinism.
On 11/03/16 09:18, Ricardo Wurmus wrote:
> + (description
> + "CD-HIT is a program for clustering and comparing protein or nucleotide
> +sequences. CD-HIT is very fast and can handle extremely large databases.
> +CD-HIT helps to significantly reduce the computational and manual efforts in
> +many sequence analysis tasks and aids in understanding the data structure and
> +correct the bias within a dataset.")
I didn't understand that last sentence, and I thought the 2nd sentence
was a bit too opinionated. In my patch the description was simply:
+ (description
+ "CD-HIT is a program for clustering and comparing protein or
nucleotide
+sequences. CD-HIT is designed to be fast and handle extremely large
+databases.")
HTH,
ben
^ permalink raw reply [flat|nested] 5+ messages in thread
* [PATCH} Add cd-hit.
@ 2016-02-21 11:02 Ben Woodcroft
2016-02-23 13:24 ` Ludovic Courtès
2016-02-23 13:33 ` Ricardo Wurmus
0 siblings, 2 replies; 5+ messages in thread
From: Ben Woodcroft @ 2016-02-21 11:02 UTC (permalink / raw)
To: guix-devel@gnu.org
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Thanks in advance.
[-- Attachment #2: 0001-gnu-Add-cd-hit.patch --]
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From 95ae898345774f6bb26ce11a340b688118d6c4ba Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 16 Jan 2016 14:31:25 +1000
Subject: [PATCH] gnu: Add cd-hit.
* gnu/packages/bioinformatics.scm (cd-hit): New variable.
---
gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a72765a..87b2519 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -807,6 +807,46 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for
multiple sequence alignments.")
(license license:expat)))
+(define-public cd-hit
+ (package
+ (name "cd-hit")
+ (version "4.6.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/weizhongli/cdhit/releases/download/V"
+ version
+ "/cd-hit-v"
+ version
+ "-2015-0603.tar.gz"))
+ (sha256
+ (base32
+ "0b6r52hhz3apx3wbc3zpzmxzyv6p7n3w4x3didadsjbnnav5006a"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no tests
+ #:make-flags
+ (list (string-append "PREFIX="
+ (assoc-ref %outputs "out")
+ "/bin"))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'install 'create-output-directory
+ (lambda* (#:key outputs #:allow-other-keys)
+ (mkdir-p (string-append
+ (assoc-ref outputs "out") "/bin")))))))
+ (inputs
+ `(("perl" ,perl)))
+ (home-page "http://weizhongli-lab.org/cd-hit/")
+ (synopsis "Cluster and compare protein or nucleotide sequences")
+ (description
+ "CD-HIT is a program for clustering and comparing protein or nucleotide
+sequences. CD-HIT is designed to be fast and handle extremely large
+databases.")
+ (license license:gpl2)))
+
(define-public clipper
(package
(name "clipper")
--
2.6.3
^ permalink raw reply related [flat|nested] 5+ messages in thread
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2016-03-11 14:18 [PATCH] Add CD-HIT Ricardo Wurmus
2016-03-11 16:02 ` Ben Woodcroft
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2016-02-21 11:02 [PATCH} Add cd-hit Ben Woodcroft
2016-02-23 13:24 ` Ludovic Courtès
2016-02-23 13:33 ` Ricardo Wurmus
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