[Debian-med-packaging] Package GMAP and GSNAP

[Shaun Jackman]

Hi Andreas,

There's two related executables in the same source package, GMAP and
GSNAP. There's also a bunch of auxiliary executables that relate to
both packages. Do you think we should create three binary packages
(gmap, gsnap, common) or one binary package?

Should the source package be named gmap-gsnap or gmap? The upstream
source is named
gmap-gsnap-2010-03-09.tar.gz

If one binary package, should it be named gmap-gsnap or gmap?

If three binary packages, should the common stuff be named gmap-gsnap
or gmap-gsnap-common? (or something else)

A list of the executables follows. I'm a little concerned that
executables such as snpindex are named too generically. Perhaps all
the auxiliary executables should be put in /usr/lib/gmap (or
/usr/lib/gmap-gsnap?).

I'm leaning towards naming the source package gmap (rather than gmap-gsnap).

Cheers,
Shaun

-rwxr-xr-x root/root   1592096 2010-04-28 17:56 ./usr/bin/cmetindex
-rwxr-xr-x root/root     90000 2010-04-28 17:56 ./usr/bin/dibaseindex
-rwxr-xr-x root/root     11803 2010-04-28 17:56 ./usr/bin/fa_coords
-rwxr-xr-x root/root    108916 2010-04-28 17:56 ./usr/bin/get-genome
-rwxr-xr-x root/root   1143176 2010-04-28 17:56 ./usr/bin/gmap
-rwxr-xr-x root/root     10450 2010-04-28 17:56 ./usr/bin/gmap_compress
-rwxr-xr-x root/root      3345 2010-04-28 17:56 ./usr/bin/gmap_process
-rwxr-xr-x root/root       543 2010-04-28 17:56 ./usr/bin/gmap_reassemble
-rwxr-xr-x root/root     18931 2010-04-28 17:56 ./usr/bin/gmap_setup
-rwxr-xr-x root/root     16452 2010-04-28 17:56 ./usr/bin/gmap_uncompress
-rwxr-xr-x root/root    105496 2010-04-28 17:56 ./usr/bin/gmapindex
-rwxr-xr-x root/root   4508772 2010-04-28 17:56 ./usr/bin/gsnap
-rwxr-xr-x root/root     96548 2010-04-28 17:56 ./usr/bin/gsnap_tally
-rwxr-xr-x root/root     59284 2010-04-28 17:56 ./usr/bin/iit_dump
-rwxr-xr-x root/root     72116 2010-04-28 17:56 ./usr/bin/iit_get
-rwxr-xr-x root/root     47748 2010-04-28 17:56 ./usr/bin/iit_store
-rwxr-xr-x root/root     29296 2010-04-28 17:56 ./usr/bin/md_coords
-rwxr-xr-x root/root    104380 2010-04-28 17:56 ./usr/bin/snpindex


On 28 April 2010 13:48, Andreas Tille <andreas at fam-tille.de> wrote:
> On Wed, Apr 28, 2010 at 11:03:13AM -0700, Shaun Jackman wrote:
>> Could GMAP (the gapped aligner) be packaged?
>> http://research-pub.gene.com/gmap/
>
> Sure - the license seems to be DFSG free, so why not.
>
>> Should I submit an RFP, or post a request on the wiki?
>
> My (>10 years) experience has shown that RFPs are in most cases not
> successfull and a request on the wiki (which page???) also has probably
> not the best chances.  For Debian Med we are using the so called
> tasks pages from the Blends framework and I just added gmap to
>
>  svn://svn.debian.org/svn/blends/projects/med/trunk/debian-med/tasks/bio
>
> which will automatically turned into an entry at
>
>  http://debian-med.alioth.debian.org/tasks/bio#gmap
>
> My attempt to provide a description is quite weak.  You seem to know the
> program better - so any DD has commit permissions to the SVN above and I
> would really invite you to enhance this.  IT is a good preparation for
> an ITP or a control file and so this time is not wasted.
>
>> I could potentially take on this packaging myself. If that's desired,
>
> Yes, this would be really welcome!
>
>> where should I start?
>
> Just have a look into the Debian Med policy
>
>   http://debian-med.alioth.debian.org/docs/policy.html
>
> and ask on the list if something remains unclear.  If you are working in
> the field of medicine / biology it would be great if you would subscribe
> debian-med at lists.debian.org (and send a short introduction of yourself to
> the list).
>
>> I am a Debian developer.
>
> That's good and makes some technical things (Vcs commits, upload of
> packages more smooth).
>
> We would be really happy if you would join our team
>
>    Andreas.
>
> --
> http://fam-tille.de
>