Re: Update on Trinityrnaseq packaging
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Hi Michael,
On Thu, Feb 12, 2015 at 09:42:45PM +0000, Michael Crusoe wrote:
> > ...
> > code I have seen (not too much admittedly) had extra *.so files in
> > /usr/lib. If you are unsure asking on debian-java@lists.debian.org is
> > the best way to clarify.
>
> Upon review they are pure Java
:-)
> > > - [ ] binary-without-manpage usr/bin/Trinity
> >
> > Same as above. It would be nice to have (even nicer than hardening)
> > there are cases where it is hard to write a sensible manpage.
>
> I've produced one with help2man.
That's usually the cheapest way and fine for the most cases.
Unfortunately it did not worked in this case - I commited a manually
edited manpage based on yours. The result at least fits nroff syntax.
:-)
> > > - [ ] script-not-executable: several
> >
> > Usually this is either easy to fix or contains a hidden problem that
> > should be fixed.
>
> Fixed
Good!
> > * `licensecheck -r *` did not uncover anything suspicious to me
> > * trinity-plugins/GAL_0.2.1: This third party code should be
> > specified separately with the license that can be found in the
> > downloadable archive at
> > http://www.sequenceontology.org/software/GAL_Code/
> > However, I'd prefer packaging GAL separately (in the latest
> > version)
>
> Sure, for another day :-)
:-)
> > * trinity-plugins/Trimmomatic-0.32: Binary without source!
> > Trimmomatic is packaged in this version anyway - so this should
> > be simply dropped via Files-Excluded
> >
>
> Done
OK - but the dir remains in the Git repository. You should import
a cleaned up archive. You can get this by
debian/rules get-orig-source
... or if you want to save your bandwidth via
mk-origtargz --repack --compress xz <path_to_original_download_source>
Afterwards do
git import-orig --pristine-tar <path_to_your_2.0.3+dfsg_tar>
> > * trinity-plugins/collectl: Packaged for Debian. Once you are
> > removing files via Files-Excluded the most easy thing would be
> > to delete this as well which saves you the work of mentioning
> > it in d/copyright
>
> Only used via a hidden option. Excluded and added as a 'suggests'
If you are sure that it should not be Recommends that's fine for me.
> > * trinity-plugins/fstrozzi-Fastool-7c3e034f05: While mentioned
> > properly in d/copyright I'd at least refer to the download
> > location
> > https://github.com/fstrozzi/Fastool
> > in a Comment: field. I'd regard it as the better solution to
> > create a separate package since it might be considered useful
> > for people not only using it via trinityrnaseq
>
> I've added the comment. As for packaging it separately I'll leave this to
> some other motivated individual to do so. There are a lot of bioinformatics
> libraries that are functionally single use.
May be I'll care for this in some MoM project. Usually these small
tools are easy targets and than it should be done also for the sake of
separate testing.
> > * trinity-plugins/parafly/src/ParaFly.cpp:
> > Authors of this wrapper are MB Couger (mbcouger(AT Symbol)gmail.com,
> > Matt Stowe mstowe(AT Symbol)okstate.edu
> > This should at least deserve an extra d/copyright line and you
> > should also dig for the original download location. I can
> > not evaluate the sense of a separate package.
> >
>
> Nothing coming up. Probably Broad Foundation employees / interns. I think
> they are covered by the existing entry.
Finally it does not matter what you think but what you can convince
ftpmaster to accept. ;-)
> > * trinity-plugins/slclust: Same as for Fasttool - I'd really
> > love to see a separate package from
> > http://sourceforge.net/projects/slclust/
>
> See above :-)
Yup.
> > * trinity-plugins/TransDecoder_r20140704.tar.gz:
> > Same as for Fasttool / slclust:
> > https://transdecoder.github.io/
>
>
> Gah, this contains two programs already packaged (cd-hit & ffindex (two
> versions!)) and another copy of Parafly. Looks like this will require a
> separate package just to keep the source clean. Trinity can use the Parafly
> from this (yet to be created) package.
Sometimes the packaging view uncovers this kind of ugly things ...
> > * trinity-plugins/jellyfish-2.1.4.tar.gz: --> Files-Excluded
> > since we have a separate package
> > * trinity-plugins/rsem-1.2.19.tar.gz: --> Files-Excluded since
> > you ITP it as you wrote below
>
> Done.
OK.
> > Please feel free to ask for help here if you agree that Fastool, slclust
> > and transdecoder should be packaged separately. I could even try to
> > work in a MoM project with some potential student on these.
> >
> > > trinityrnaseq has two unfulfilled dependencies: rsem & express
> > >
> > > rsem
> > > - [ ] lacks manpages
> > > - [ ] lacks ITP
> > >
> > > express:
> > > - [ ] lacks ITP
> >
> > Thanks for sending this kind of status messages. That's really helpful
> > and enables team input.
>
> Go team!
... nice you like the cooperation
Andreas.
--
http://fam-tille.de
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