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Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 38 |
1 files changed, 38 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f5e7285193..22eba0f6a3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3359,6 +3359,44 @@ 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 (pypi-uri "screed" version)) + (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 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") |