From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Add python2-seqmagick. Date: Thu, 17 Sep 2015 17:51:23 +0200 Message-ID: References: <55FAA83C.3040403@uq.edu.au> Mime-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:46406) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZcbTD-000622-PW for guix-devel@gnu.org; Thu, 17 Sep 2015 11:51:36 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZcbTA-0004uK-JA for guix-devel@gnu.org; Thu, 17 Sep 2015 11:51:35 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:56800) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZcbTA-0004u1-5L for guix-devel@gnu.org; Thu, 17 Sep 2015 11:51:32 -0400 In-Reply-To: <55FAA83C.3040403@uq.edu.au> 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-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Ben Woodcroft Cc: "guix-devel@gnu.org" Hi Ben, thank you very much for your patch! > From 298c9aabc2d042c45c8f96d83229016dc5c1cbd6 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Thu, 17 Sep 2015 21:43:12 +1000 > Subject: [PATCH] gnu: Add python2-seqmagick. > * gnu/packages/bioinformatics.scm (python2-seqmagick): New variable. Maybe this should be just called =E2=80=9Cseqmagick=E2=80=9D. It=E2=80=99= s written in Python, but since it=E2=80=99s not a library I don=E2=80=99t think it needs to ha= ve the =E2=80=9Cpython2-=E2=80=9D prefix. > +(define-public python2-seqmagick > + (package > + (name "python2-seqmagick") > + (version "0.6.1") > + (source > + (origin > + (method url-fetch) > + (uri (string-append > + "https://pypi.python.org/packages/source/s/seqmagick/seqm= agick-" > + version ".tar.gz")) > + (sha256 > + (base32 > + "0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d")))) > + (build-system python-build-system) > + (arguments > + ;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56 > + `(#:python ,python-2 > + #:phases > + (modify-phases %standard-phases > + ;; current test in setup.py does not work as of 0.6.1, > + ;; so use nose to run tests instead for now. See > + ;; https://github.com/fhcrc/seqmagick/issues/55 > + (replace 'check (lambda _ (zero? (system* "nosetests"))))))) > + (inputs > + `(("python-setuptools" ,python2-setuptools) I think this should be a native input instead. > + ("python-biopython" ,python2-biopython))) And this looks like it should be a propagated input instead. Have you tried running seqmagick after installing it with this package recipe? I found that Python executables often require either propagated inputs or wrapping in PYTHONPATH to work without runtime errors. > + (native-inputs > + `(("python-nose" ,python2-nose))) > + (home-page "http://github.com/fhcrc/seqmagick") > + (synopsis > + "Tools for converting and modifying sequence files from the comma= nd-line") The synopsis is a bit long. You could shave off two words like this: =E2=80=9CCommand-line tools for converting and modifying sequence files= =E2=80=9D but that=E2=80=99s not really much better. I=E2=80=99m open to suggestio= ns. > + (description > + "Bioinformaticians often have to convert sequence files between f= ormats > +and do little manipulations on them, and it's not worth writing script= s for > +that. Seqmagick is a utility to expose the file format conversion in > +BioPython in a convenient way. Instead of having a big mess of script= s, there > +is one that takes arguments.") > + (license license:gpl3))) > + I=E2=80=99m not sure if it=E2=80=99s really =E2=80=9CGPLv3 only=E2=80=9D = or =E2=80=9CGPLv3 or later=E2=80=9D as there are no license headers anywhere. Maybe others could comment what=E2=80=99= s the proper declaration here. ~~ Ricardo