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[PATCH 2/3] gnu: Add python-screed.
From: |
Ben Woodcroft |
Subject: |
[PATCH 2/3] gnu: Add python-screed. |
Date: |
Sat, 18 Jun 2016 08:33:31 +1000 |
* gnu/packages/bioinformatics.scm (python-screed, python2-screed):
New variables.
---
gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 04ed769..76a6ebc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3359,6 +3359,42 @@ 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
+ (pypi-origin
+ "screed" version ".tar.gz"
+ "a06ba90c7ab7b0ad1eab211053c85c1242a81379f34c5f5933392079c9b36858"
+ "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 database utilities")
+ (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