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