diff mbox

[1/3] gnu: Add python-screed.

Message ID 1466126601-30932-2-git-send-email-donttrustben@gmail.com
State New
Headers show

Commit Message

Ben Woodcroft June 17, 2016, 1:23 a.m. UTC
* gnu/packages/bioinformatics.scm (python-screed, python2-screed):
New variables.
---
 gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

Comments

Leo Famulari June 17, 2016, 2:07 a.m. UTC | #1
On Fri, Jun 17, 2016 at 11:23:19AM +1000, Ben Woodcroft wrote:
> * gnu/packages/bioinformatics.scm (python-screed, python2-screed):
> New variables.

> +       (uri (string-append
> +             "https://pypi.python.org/packages/a0/6b/"
> +             "a90c7ab7b0ad1eab211053c85c1242a81379f34c5f5933392079c9b36858"

Can you keep the hash on a single line? Just to reduce noise in the
commit log for future updates...

> +    (synopsis "Short read sequence utils")

s/utils/utilities

> +    (description "Screed parses FASTA and FASTQ files and generates databases.

Can you unpack these acronyms?
Ben Woodcroft June 17, 2016, 10:57 p.m. UTC | #2
On 17/06/16 12:07, Leo Famulari wrote:
> On Fri, Jun 17, 2016 at 11:23:19AM +1000, Ben Woodcroft wrote:
>> * gnu/packages/bioinformatics.scm (python-screed, python2-screed):
>> New variables.
>> +       (uri (string-append
>> +             "https://pypi.python.org/packages/a0/6b/"
>> +             "a90c7ab7b0ad1eab211053c85c1242a81379f34c5f5933392079c9b36858"
> Can you keep the hash on a single line? Just to reduce noise in the
> commit log for future updates...

OK.

>
>> +    (synopsis "Short read sequence utils")
> s/utils/utilities

"database utilities" would be even better I think.

>
>> +    (description "Screed parses FASTA and FASTQ files and generates databases.
> Can you unpack these acronyms?

Acronyms are no fun in descriptions I agree. But the problem here is 
that FASTA and FASTQ aren't really acronyms, and besides these terms are 
extremely well known (like 'tar' or 'zip').

On a side note, FASTA was first used by the "FASTA" program circa 1985 
(just like I am). And just like me it is still going - last release was 
April. I might have a go at packaging it.

ben
diff mbox

Patch

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")