Re: [PATCH] Add python2-seqmagick.

[Ben Woodcroft]

On 18/09/15 01:51, Ricardo Wurmus wrote:

Hi Ben,

thank you very much for your patch!

and you sir, for the review.

+    (inputs
+     `(("python-setuptools" ,python2-setuptools)

I think this should be a native input instead.

ok

+       ("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.

I did, although not well enough to pick up the error you point out. Actually I'm a bit confused as to the difference between the input types even after reading the manual. Is this a fair summary?

native-inputs: required for building but not runtime - installing a package through a substitute won't install these inputs
inputs: installed in the store but not in the profile, as well as being present at build time
propagated-inputs: installed in the store and in the profile, as well as being present at build time


Anyway, it seems as if the package would have worked because a wrapper is generated with PYTHONPATH including inputs, propagated-inputs and native-inputs. But this seems a bit strange - why would native inputs be in the runtime wrapper?

$ cat /tmp/a.fa
>a
ATGG
$ ./pre-inst-env guix environment --ad-hoc seqmagick --pure -E 'echo $PATH; echo $PYTHONPATH; seqmagick info /tmp/a.fa'
;;; note: source file /home/ben/git/guix/gnu/packages/bioinformatics.scm
;;;       newer than compiled /home/ben/git/guix/gnu/packages/bioinformatics.go
/gnu/store/bjd27hqk0wnh28nzmawjymdh3gfk98pn-seqmagick-0.6.1/bin

name      alignment    min_len   max_len   avg_len  num_seqs
/tmp/a.fa FALSE              4         4      4.00         1



$ cat /gnu/store/bjd27hqk0wnh28nzmawjymdh3gfk98pn-seqmagick-0.6.1/bin/.seqmagick-wrap-01
#!/gnu/store/cpx9iibpdwi3wb81glpnnlxr9zra2iiv-bash-4.3.39/bin/bash
export PYTHONPATH="/gnu/store/bjd27hqk0wnh28nzmawjymdh3gfk98pn-seqmagick-0.6.1/lib/python2.7/site-packages:/gnu/store/qlf4k2b81wms6avlyny7hix175asg8kg-python-2.7.10/lib/python2.7/site-packages:/gnu/store/zmhk5r3lmc3s8ivdx9vv6m5vzn6fqim5-python2-setuptools-12.1/lib/python2.7/site-packages:/gnu/store/20s2vvslsapynhmbfsa3q2iyv9dzjzr2-python2-nose-1.3.4/lib/python2.7/site-packages:/gnu/store/c7navsrzibg2rjgs1fzqry711wch5f3p-python2-biopython-1.65/lib/python2.7/site-packages:/gnu/store/bjd27hqk0wnh28nzmawjymdh3gfk98pn-seqmagick-0.6.1/lib/python2.7/site-packages/${PYTHONPATH:+:}$PYTHONPATH"
exec -a "$0" "/gnu/store/bjd27hqk0wnh28nzmawjymdh3gfk98pn-seqmagick-0.6.1/bin/.seqmagick-real" "$@"

+    (native-inputs
+     `(("python-nose" ,python2-nose)))
+    (home-page "http://github.com/fhcrc/seqmagick")
+    (synopsis
+     "Tools for converting and modifying sequence files from the command-line")

The synopsis is a bit long.  You could shave off two words like this:

  “Command-line tools for converting and modifying sequence files”

but that’s not really much better.  I’m open to suggestions.

"Tools for converting and modifying sequence files"

+    (description
+     "Bioinformaticians often have to convert sequence files between formats
+and do little manipulations on them, and it's not worth writing scripts 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 scripts, there
+is one that takes arguments.")
+    (license license:gpl3)))
+

I’m not sure if it’s really “GPLv3 only” or “GPLv3 or later” as there
are no license headers anywhere.  Maybe others could comment what’s the
proper declaration here.

From the readme:
>seqmagick is free software under the GPL v3.

Is that not straightforward enough?

Thanks,
ben

0001-gnu-Add-seqmagick.patch
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