No problem about the users not necessarily respecting the license. We already have the source code up on the net with no protection. We rely on the honor system, and the business remains good enough at least to pay the mortgage.
I think there may be a problem with your build. I've got a _little_ time to help you with this, but if I get too busy to answer all your email please don't take it personally. Here's the output I get from the make test in our main source tree. blat -verbose=0 hCrea.geno hCrea.mrna testRna.psl Loaded 6896 letters in 1 sequences Searched 1540 bases in 1 sequences cmp testRna.psl refRna.psl blat -verbose=0 -prot hCrea.pep mCrea.pep testProt.psl Loaded 417 letters in 1 sequences Searched 418 bases in 1 sequences cmp testProt.psl refProt.psl blat -verbose=0 -t=dnax -q=prot hCrea.geno mCrea.pep testProtX.psl Loaded 6896 letters in 1 sequences Blatx 1 sequences in database, 1 files in query cmp testProtX.psl refProtX.psl blat -verbose=0 -t=dnax -q=rnax hCrea.geno mCrea.mrna testRnaX.psl Loaded 6896 letters in 1 sequences Blatx 1 sequences in database, 1 files in query cmp testRnaX.psl refRnaX.psl blat -verbose=0 -fine hCrea.geno hCrea.mrna testFine.psl Loaded 6896 letters in 1 sequences Searched 1540 bases in 1 sequences cmp testFine.psl refFine.psl cd test && make make[1]: Entering directory `/cluster/home/kent/kent/src/blat/test' 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 blat -verbose=0 v29skips/ex2_database.fa v29skips/ex2_query.fa v29skips/ex2.psl Loaded 4186 letters in 1 sequences Searched 4185 bases in 1 sequences diff v29skips/ex2_reference.psl v29skips/ex2.psl 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 blat -verbose=0 intron50k/target.fa intron50k/query.fa intron50k/out/test2.psl -minScore=190 -maxIntron=40000 Loaded 100000 letters in 1 sequences Searched 600 bases in 1 sequences diff intron50k/expected/test2.psl intron50k/out/test2.psl blat -verbose=0 intron50k/target.fa intron50k/query.fa intron50k/out/test3.psl -minScore=190 -maxIntron=5000 Loaded 100000 letters in 1 sequences Searched 600 bases in 1 sequences diff intron50k/expected/test3.psl intron50k/out/test3.psl rm -rf intron50k/out make[1]: Leaving directory `/cluster/home/kent/kent/src/blat/test' On Tue, Feb 25, 2014 at 12:12 PM, Andreas Tille <[email protected]> wrote: > 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 >
