Re: Packaging BLAT for Debian

Thanks for packaging it up, and respecting the license.

You can get pslCheck in executable form for several OS's at

http://hgdownload.cse.ucsc.edu/admin/exe

The source sadly is still not isolated from the huge UCSC kent source tree. It is pretty fast to build at least though, and once you have MACHTYPE set up easy to make. Please see

http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads

to get the whole source tree.

On Mon, Feb 24, 2014 at 2:51 PM, Andreas Tille <andreas@an3as.eu> wrote:

Hi Jim,

I'm writing you on behalf of the Debian Med team that has the goal to
introduce official Debian packages of Free Software which is relevant
in medicine and biology. Considering that you are the author of BLAT
you might be interested in our biology task here

http://blends.debian.org/med/tasks/bio

to get an overview what we are working on.

You might have noticed that also your software BLAT is mentioned on
this page

http://blends.debian.org/med/tasks/bio#blat

on out todo list. Please note that it needs to go in Debian's non-free
section since it is restricted to scientific use only.

The problem I currently have is that I try to run any test suite of
software if it is available. So I also tried

cd blat/test; make

which quickly ends up in

blat -verbose=0 throwback/target1.fa throwback/query1.fa throwback/test.psl
Loaded 129433 letters in 1 sequences
Searched 2050 bases in 1 sequences
pslCheck -verbose=0 throwback/test.psl
make: pslCheck: Command not found
make: *** [tThrowback] Error 127

since there is no binary pslCheck. Did I missed something when creating
the binaries from BLAT source since I only found a function

int pslCheck(char *pslDesc, FILE* out, struct psl* psl)

in file lib/psl.c but no such executable to call. Any hint how to
run the test suite successfully?

Kind regards and thanks for providing BLAT

Andreas.

--
http://fam-tille.de