Re: Update on Trinityrnaseq packaging
On Thu, Feb 12, 2015 at 12:16:57AM +0000, Michael Crusoe wrote:
> - [ ] hardening-no-relro usr/lib/trinityrnaseq/Chrysalis/*
> Needs investigation
While fixing this is nice to have I would not insist on it for sponsoring
> - [ ] jar-not-in-usr-share usr/lib/trinityrnaseq/Butterfly/Butterfly.jar,
> May be fixable with a move + symlink. Need to make sure that they are pure
I'm not a Java expert but IMHO all JARs are machine independent and thus
should reside in /usr/share. All Java packages with machine dependant
code I have seen (not too much admittedly) had extra *.so files in
/usr/lib. If you are unsure asking on email@example.com is
the best way to clarify.
> - [ ] 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.
> - [ ] script-not-executable: several
Usually this is either easy to fix or contains a hidden problem that
should be fixed.
> - [ ] debian/copyright needs audit
* lacking "Files: debian/*" paragraph
* `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
However, I'd prefer packaging GAL separately (in the latest
* trinity-plugins/Trimmomatic-0.32: Binary without source!
Trimmomatic is packaged in this version anyway - so this should
be simply dropped via Files-Excluded
* 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
* trinity-plugins/fstrozzi-Fastool-7c3e034f05: While mentioned
properly in d/copyright I'd at least refer to the download
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
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.
* trinity-plugins/slclust: Same as for Fasttool - I'd really
love to see a separate package from
Same as for Fasttool / slclust:
* 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
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
> - [ ] lacks manpages
> - [ ] lacks ITP
> - [ ] lacks ITP
Thanks for sending this kind of status messages. That's really helpful
and enables team input.