From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: guix-devel <guix-devel@gnu.org>
Subject: [PATCH] gnu: Add bowtie.
Date: Tue, 16 Dec 2014 18:07:41 +0100 [thread overview]
Message-ID: <idjwq5r5xr6.fsf@bimsb-sys02.mdc-berlin.net> (raw)
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Attached is a patch to add bowtie to the bioinformatics module. The
test suite depends on a couple of Perl modules for which I have
previously submitted patches:
- [[http://lists.gnu.org/archive/html/guix-devel/2014-12/msg00326.html][Test::Simple]]
- [[http://lists.gnu.org/archive/html/guix-devel/2014-12/msg00321.html][Test::Deep]]
- [[http://lists.gnu.org/archive/html/guix-devel/2014-12/msg00323.html][Clone]]
-- rekado
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From 713bb1145ff901c4069f2fadb210d8eb842981da Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 16 Dec 2014 17:52:44 +0100
Subject: [PATCH] gnu: Add bowtie
* gnu/packages/bioinformatics.scm (bowtie): New variable.
---
gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 60 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6f6178a..755287d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -28,6 +28,66 @@
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python))
+(define-public bowtie
+ (package
+ (name "bowtie")
+ (version "2.2.4")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn"))))
+ (build-system gnu-build-system)
+ (inputs `(("perl" ,perl)
+ ("perl-clone" ,perl-clone)
+ ("perl-test-deep" ,perl-test-deep)
+ ("perl-test-simple" ,perl-test-simple)
+ ("python" ,python-2)))
+ (arguments
+ '(#:make-flags '("allall")
+ #:phases
+ (alist-cons-after
+ 'unpack
+ 'patch-makefile
+ (lambda _
+ (substitute* "Makefile"
+ (("^CC = .*$") (string-append "CC = " (which "gcc")))
+ (("^CPP = .*$") (string-append "CPP = " (which "g++")))
+ ;; replace BUILD_HOST and BUILD_TIME for deterministic build
+ (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
+ (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))
+ (alist-delete
+ 'configure
+ (alist-replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (mkdir-p bin)
+ (for-each (lambda (file)
+ (copy-file file (string-append bin file)))
+ (find-files "." "bowtie2.*"))))
+ (alist-replace
+ 'check
+ (lambda* (#:key outputs #:allow-other-keys)
+ (system* "perl"
+ "scripts/test/simple_tests.pl"
+ "--bowtie2=./bowtie2"
+ "--bowtie2-build=./bowtie2-build"))
+ %standard-phases))))))
+ (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
+ (synopsis "Fast and sensitive nucleotide sequence read aligner")
+ (description
+ "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
+reads to long reference sequences. It is particularly good at aligning reads
+of about 50 up to 100s or 1,000s of characters, and particularly good at
+aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
+genome with an FM Index to keep its memory footprint small: for the human
+genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
+gapped, local, and paired-end alignment modes.")
+ (license license:gpl3)))
+
(define-public samtools
(package
(name "samtools")
--
1.9.3
next reply other threads:[~2014-12-16 17:08 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-12-16 17:07 Ricardo Wurmus [this message]
2014-12-17 20:41 ` [PATCH] gnu: Add bowtie Ludovic Courtès
2014-12-18 16:15 ` Ricardo Wurmus
2014-12-19 17:52 ` Ludovic Courtès
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