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 [[email protected]] 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 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
