From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Add python2-seqmagick. Date: Fri, 25 Sep 2015 16:09:39 +0200 Message-ID: References: <55FAA83C.3040403@uq.edu.au> <55FD2C91.9080203@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]:43468) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZfThA-0007nc-SH for guix-devel@gnu.org; Fri, 25 Sep 2015 10:09:58 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZfTh6-0007Pd-Rf for guix-devel@gnu.org; Fri, 25 Sep 2015 10:09:52 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:40647) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZfTh6-0007OO-FQ for guix-devel@gnu.org; Fri, 25 Sep 2015 10:09:48 -0400 In-Reply-To: <55FD2C91.9080203@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" Ben Woodcroft writes: >>> + ("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 o= r >> wrapping in PYTHONPATH to work without runtime errors. > > I did, although not well enough to pick up the error you point out.=20 > Actually I'm a bit confused as to the difference between the input type= s=20 > even after reading the manual. Is this a fair summary? I=E2=80=99m sorry to have confused you here. =E2=80=9Cbiopython=E2=80=9D= should *not* be a propagated input here, because =E2=80=9Cseqmagick=E2=80=9D provides an ex= ecutable, not a library. I was not aware of the fact that the executables are automatically wrapped here (although the PYTHONPATH is a little too broad as you also noted). > Anyway, it seems as if the package would have worked because a wrapper=20 > is generated with PYTHONPATH including inputs, propagated-inputs and=20 > native-inputs. But this seems a bit strange - why would native inputs b= e=20 > in the runtime wrapper? Good question. I think it=E2=80=99s because the wrapping phase just wrap= s the scripts in =E2=80=9C$out/bin=E2=80=9D with whatever the PYTHONPATH variab= le contains. It doesn=E2=80=99t construct a minimally sufficient PYTHONPATH. Maybe th= at=E2=80=99s worth changing in the python-build-system? >>> + (synopsis >>> + "Tools for converting and modifying sequence files from the com= mand-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 f= iles=E2=80=9D >> >> but that=E2=80=99s not really much better. I=E2=80=99m open to sugges= tions. > "Tools for converting and modifying sequence files" That=E2=80=99s okay. >>> + (description >>> + "Bioinformaticians often have to convert sequence files between= formats >>> +and do little manipulations on them, and it's not worth writing scri= pts for >>> +that. Seqmagick is a utility to expose the file format conversion i= n >>> +BioPython in a convenient way. Instead of having a big mess of scri= pts, 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= =99s the >> proper declaration here. > From the readme: > >|seqmagick| is free software under the GPL v3. > > Is that not straightforward enough? I=E2=80=99m still not sure, but the explicit mention of =E2=80=9Cv3=E2=80= =9D is enough for me to not write =E2=80=9Cgpl3+=E2=80=9D here. I=E2=80=99ll push your latest patch with minor modifications (undoing the =E2=80=9Cpropagated-inputs=E2=80=9D confusion I caused and moving the syn= opsis on one line). Thanks again! ~~ Ricardo