From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH 2/3] gnu: Add python-screed. Date: Sat, 18 Jun 2016 08:33:31 +1000 Message-ID: <1466202812-18604-3-git-send-email-donttrustben@gmail.com> References: <87oa8v2q7x.fsf@gnu.org> <1466202812-18604-1-git-send-email-donttrustben@gmail.com> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:54473) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bE2L1-0005xG-Bg for guix-devel@gnu.org; Fri, 17 Jun 2016 18:34:08 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bE2Ku-0008EW-Vb for guix-devel@gnu.org; Fri, 17 Jun 2016 18:34:06 -0400 In-Reply-To: <1466202812-18604-1-git-send-email-donttrustben@gmail.com> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: ludo@gnu.org, guix-devel@gnu.org * 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