Re: Packaging BLAT for Debian
Hi Jim,
thanks for your quick and helpful response.
On Tue, Feb 25, 2014 at 09:28:04AM -0800, Jim Kent wrote:
> Thanks for packaging it up, and respecting the license.
Sure Debian as a distribution will respect the license. It is also
quite verbosely included in any package. However, for sure we have no
influence whether any *user* will respect 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.
Ahhh, I started fighting through the list of dependencies but it seems
to be complex (so yes, I might understand your reasons not to inject
it into the BLAT source). However, *if* we want to run the test inside
Debian we would really need the source since we can not distribute
binaries. Ignoring this for a moment I simply used the binary to find
out whether the test would run at all.
cd blat/test; make tThrowback
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
blat -verbose=0 v29skips/ex1_database.fa v29skips/ex1_query.fa v29skips/ex1.psl
Loaded 4481 letters in 1 sequences
Searched 4484 bases in 1 sequences
diff v29skips/ex1_reference.psl v29skips/ex1.psl
6c6
< 4478 3 0 0 1 3 0 0 + genomicMrnaSCA2 4484 0 4484 FnaSCA2 4481 0 4481 2 699,3782, 0,702, 0,699,
---
> 3782 0 0 0 0 0 0 0 + genomicMrnaSCA2 4484 702 4484 FnaSCA2 4481 699 4481 1 3782, 702, 699,
make: *** [tThrowback] Error 1
Trying the second check is not working any better:
$ make tIntronMax
mkdir -p intron50k/out
blat -verbose=0 intron50k/target.fa intron50k/query.fa intron50k/out/test1.psl -minScore=190
Loaded 100000 letters in 1 sequences
Searched 600 bases in 1 sequences
diff intron50k/expected/test1.psl intron50k/out/test1.psl
6c6,8
< 600 0 0 0 0 0 2 60200 + query 600 0 600 chr16part 100000 10000 70800 3 200,199,201, 0,200,399, 10000,60200,70599,
---
> 542 9 0 0 0 0 3 67695 + query 600 0 551 chr16part 100000 10000 78246 4 200,199,81,71, 0,200,399,480, 10000,60200,70599,78175,
> 202 0 0 0 0 0 0 0 + query 600 200 402 chr16part 100000 60200 60402 1 202, 200, 60200,
> 201 0 0 0 0 0 0 0 + query 600 399 600 chr16part 100000 70599 70800 1 201, 399, 70599,
make: *** [tIntronMax] Error 1
I wonder whether you are aware about circumstances when these both tests
are failing and what this might mean for the blat executable I created
on a Debian machine on amd64 architecture (using MACHTYPE="x86_64").
Does this mean that my build was faulty or is there any other problem?
Kind regards
Andreas.
--
http://fam-tille.de
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