From: Ben Woodcroft <donttrustben@gmail.com>
To: Guix-devel@gnu.org
Subject: [PATCH 1/3] gnu: Add python-screed.
Date: Fri, 17 Jun 2016 11:23:19 +1000 [thread overview]
Message-ID: <1466126601-30932-2-git-send-email-donttrustben@gmail.com> (raw)
In-Reply-To: <1466126601-30932-1-git-send-email-donttrustben@gmail.com>
* gnu/packages/bioinformatics.scm (python-screed, python2-screed):
New variables.
---
gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 04ed769..22ed71a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3359,6 +3359,47 @@ optimize the sequencing depth, or to screen multiple libraries to avoid low
complexity samples.")
(license license:gpl3+)))
+(define-public python-screed
+ (package
+ (name "python-screed")
+ (version "0.9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/a0/6b/"
+ "a90c7ab7b0ad1eab211053c85c1242a81379f34c5f5933392079c9b36858"
+ "/screed-" version ".tar.gz"))
+ (sha256
+ (base32
+ "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (setenv "PYTHONPATH"
+ (string-append (getenv "PYTHONPATH") ":."))
+ (zero? (system* "nosetests" "--attr" "!known_failing")))))))
+ (native-inputs
+ `(("python-nose" ,python-nose)))
+ (inputs
+ `(("python-bz2file" ,python-bz2file)))
+ (home-page "http://github.com/dib-lab/screed/")
+ (synopsis "Short read sequence utils")
+ (description "Screed parses FASTA and FASTQ files and generates databases.
+Values such as sequence name, sequence description, sequence quality and the
+sequence itself can be retrieved from these databases.")
+ (license license:bsd-3)))
+
+(define-public python2-screed
+ (let ((base (package-with-python2 (strip-python2-variant python-screed))))
+ (package
+ (inherit base)
+ (native-inputs `(("python2-setuptools" ,python2-setuptools)
+ ,@(package-native-inputs base))))))
+
(define-public sra-tools
(package
(name "sra-tools")
--
2.7.4
next prev parent reply other threads:[~2016-06-17 1:23 UTC|newest]
Thread overview: 19+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-06-17 1:23 [PATCH] Add khmer Ben Woodcroft
2016-06-17 1:23 ` Ben Woodcroft [this message]
2016-06-17 2:07 ` [PATCH 1/3] gnu: Add python-screed Leo Famulari
2016-06-17 22:57 ` Ben Woodcroft
2016-06-17 1:23 ` [PATCH 2/3] gnu: Add murmur-hash Ben Woodcroft
2016-06-17 1:23 ` [PATCH 3/3] gnu: Add khmer Ben Woodcroft
2016-06-17 7:23 ` Leo Famulari
2016-06-17 23:41 ` Ben Woodcroft
2016-06-25 17:30 ` Leo Famulari
2016-06-17 8:16 ` [PATCH] " Leo Famulari
2016-06-17 9:42 ` Ben Woodcroft
2016-06-17 17:54 ` Leo Famulari
2016-06-25 17:29 ` Leo Famulari
2016-06-26 9:58 ` Ludovic Courtès
2016-06-26 11:59 ` Ben Woodcroft
2016-06-26 17:34 ` Leo Famulari
2016-06-26 22:48 ` Ben Woodcroft
2016-06-27 5:01 ` Leo Famulari
2016-06-27 5:47 ` Ben Woodcroft
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