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