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
>From 9328316f5ff7a454e0370bab9ac4897926629b72 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrust...@gmail.com>
Date: Sat, 19 Sep 2015 19:31:57 +1000
Subject: [PATCH] gnu: Add seqmagick.
* gnu/packages/bioinformatics.scm (seqmagick): New variable.
---
gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 03eb2df..08b3500 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2489,6 +2489,45 @@ manipulation, online and indexed string search, efficient I/O of
bioinformatics file formats, sequence alignment, and more.")
(license license:bsd-3)))
+(define-public seqmagick
+ (package
+ (name "seqmagick")
+ (version "0.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/source/s/seqmagick/seqmagick-";
+ 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")))))))
+ (propagated-inputs
+ `(("python-biopython" ,python2-biopython)))
+ (native-inputs
+ `(("python-setuptools" ,python2-setuptools)
+ ("python-nose" ,python2-nose)))
+ (home-page "http://github.com/fhcrc/seqmagick";)
+ (synopsis
+ "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)))
+
(define-public star
(package
(name "star")
--
2.4.3
