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[2/3] gnu: Add python-screed.

Message ID 1466202812-18604-3-git-send-email-donttrustben@gmail.com
State New
Headers show

Commit Message

Ben Woodcroft June 17, 2016, 10:33 p.m. UTC 
* gnu/packages/bioinformatics.scm (python-screed, python2-screed):
New variables.
---
 gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

Comments

Leo Famulari June 25, 2016, 5:44 p.m. UTC | #1 
On Sat, Jun 18, 2016 at 08:33:31AM +1000, Ben Woodcroft wrote:
> * gnu/packages/bioinformatics.scm (python-screed, python2-screed):

I didn't build it, but it LGTM assuming it works for you.

> +    (source
> +     (pypi-origin
> +      "screed" version ".tar.gz"
> +      "a06ba90c7ab7b0ad1eab211053c85c1242a81379f34c5f5933392079c9b36858"
> +      "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0"))

It looks like we are going to try using the pypi.io URLs instead:

http://lists.gnu.org/archive/html/guix-devel/2016-06/msg00876.html
diff mbox

Patch

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")