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 <[email protected]> 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
>
