Re: Packaging BLAT for Debian

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 <andreas@an3as.eu> 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