AW: What components of BLAT are really needed in a binary package
Hey Andreas,
I don't know about every binary, but I used blat, pslPretty, pslReps and pslSort on and a regular basis and they will all execute on their own. They don't need the web service part. And I think the converters won't, too. As far as I understand, blat is a combination of gfServer and gfClient for local use.
However, in the specifications the always refer to all binaries as the blat suite, so it seems to be intented as a package:
https://cgwb.nci.nih.gov/goldenPath/help/blatSpec.html
http://genome.ucsc.edu/goldenPath/help/blatSpec.html
I would recommend to package the hole suite since it would satisfy all possible uses cases. However, I think it possible to build a package for local purpose only by just omitting gfClient, gfServer and webBlat. I actually never downloaded them myself.
Hope this helps.
Best regards,
Mathias Kuhring
________________________________________
Von: Andreas Tille [andreas@an3as.eu]
Gesendet: Donnerstag, 20. Februar 2014 22:35
An: Debian Med Project List
Betreff: What components of BLAT are really needed in a binary package
Hi,
I received a request to package BLAT and I did some first packaging
attempt on it[1]. BLAT needs to go into non-free since it is restricted
for personal, academic, and non-profit use.
When running debuild it creates the binaries
blat, faToNib, faToTwoBit, gfClient, gfServer, nibFrag, pslPretty,
pslReps, pslSort, twoBitInfo, twoBitToFa
Since I have no idea how to reasonably use BLAT and I know there is some
web server part which is probably not needed / wanted in a user
application package I wonder whether somebody could give some hints
whether all these binaries need to be installed right into /usr/bin as
user applications. The file webBlat/install.txt which describes how to
set up a server says you should run the gfServer program to create
in-memory indexes of the databases. Is gfServer only needed if you
want to use the webserver or is it also used for local applications?
Is it correct that we do not really want a blat webserver package (since
it can be used online)?
I will use help2man to create some hopefully helpful manpages for the
binaries mentioned above in case they might all be needed.
Any comments are welcome
Andreas.
[1] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/blat/trunk/
--
http://fam-tille.de
Reply to: