Perl 6 - the future is here, just unevenly distributed

IRC log for #bioperl, 2014-04-23

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All times shown according to UTC.

Time Nick Message
01:53 scottcain joined #bioperl
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15:45 scottcain Hi All, I’m trying to track down a problem that I think is related to 1.6.923 and GBrowse.  When I run GBrowse tests, I get a bunch of messages like “MSG: No suitable files found in /var/lib/gbrowse2/databases/yeast_chr1+2” even though the GFF files are there.  Any ideas?
15:47 scottcain when running BioPerl’s tests, I get this:t/Seq/Seq.t ............................ 1/73 Can't store CODE items at Bio/Root/Root.pm line 223.
15:47 scottcain # Looks like you planned 73 tests but ran 33.
15:47 scottcain # Looks like your test exited with 255 just after 33.
15:48 cdiesh joined #bioperl
15:51 * scottcain thinks the Seq test is a red herring, but it shouldn’t happen anyway.
15:52 scottcain Also, Bio::DB::SeqFeature::Store::memory (which is what GBrowse is using for tests) hasn’t changed in 3 years, so it’s something deeper.
15:54 cdiesh i am actually seeing the same problem as scottcain on JBrowse(not GBrowse) for it's biodb-to-json tests
15:57 cdiesh this is the error i get on ubuntu related to the yeast1+2 tests. from jbrowse's setup.log: http://nopaste.info/61859e39db.html
16:18 scottcain BP 1.6.922 still does this, 1.6.901 does not.
16:55 scottcain_ joined #bioperl
17:27 trs cpantesters reports that 1.6.923 started failing on a lot more smokers
17:27 trs compare http://analysis.cpantesters.or​g/solved?distv=BioPerl-1.6.923 to http://analysis.cpantesters.or​g/solved?distv=BioPerl-1.6.922
17:27 trs er, wrong url
17:27 trs http://matrix.cpantesters.o​rg/?dist=BioPerl%201.6.922 to http://matrix.cpantesters.o​rg/?dist=BioPerl%201.6.923
17:31 trs cdiesh, scottcain: can you try the latest BioPerl from git?
17:34 cdiesh trs: i could give it a try. i haven't installed from git before though
17:35 trs cdiesh: have you used cpanm before?
17:35 cdiesh trs: yes I have used that
17:36 trs great. you should be able to install from git easily: cpanm git://github.com/bioperl/bioperl-live.git
17:36 cdiesh ah. i guess you can just give it a github URL?
17:36 trs yup
17:43 scottcain_ trs: I’ll give it a try when I get back to that machine.
17:56 cdiesh i get an error trying to install the BioPerl that Bio::Root::Build is not found, but when i try and get Bio::Root::Build it seems to download bioperl. is that a problem? trs
18:01 cdiesh this is my build.log for the bioperl-live using cpanm http://nopaste.info/3d8e992ba2.html
18:33 cdiesh i think i got it installed now..after installing an older bioperl first, and then getting the one from github
18:50 trs cdiesh: ah, yeah, it needs Bio::Root::Build to build from source. when installing from a CPAN dist, that requirement is presented to the client (cpan or cpanm) and the client installs it first beforing building bioperl itself.
18:51 trs cdiesh: also note that your cpanm log you posted indicates it installed bioperl to ~/perl5 instead of the system perl libs
18:51 trs cdiesh: run cpanm with the --sudo option to do the install as root (but the build as your own user)
18:59 cdiesh trs: i think it worked now
19:00 cdiesh is say "I think it did" because i had to rearrange some of jbrowse dependencies to make it use the cpanm library but it did not give the same error as before
19:02 cdiesh i didn't use the cpanm --sudo option, but it seems ok
19:02 cdiesh trs: do you have any estimate on when this could be released?
19:07 trs cdiesh: unfortunately not.  I'm not a bioperl committer, just someone who uses it occasionally.
19:07 trs and I do a lot of Perl. :)
19:37 scottcain_ Holy heck: cpan> install Bio::Root::Build is installing A LOT of prereqs :-)
19:41 * scottcain_ remembers that he configured cpan to install all “recommends”, so there you go.
20:18 github [bioperl-live] bosborne pushed 1 new commit to master: https://github.com/bioperl/bioperl-live/comm​it/38f56be2aa57be5351a5a1be23c07f61774e03f1
20:18 github bioperl-live/master 38f56be Brian Osborne: Minor POD edits
21:08 cdiesh trs: i think i still have the problem with the bioperl-live
21:09 cdiesh i was actually looking at the wrong file when i said it was fixed
21:10 cdiesh theres a possibility, as i said before, that it could be that i installed the old version of bioperl and then bioperl-live "over" it, but in any case i still get the error
21:42 trs cdiesh: so the issue appears to be that there's no associated fasta file containing the sequence data for the gff file
21:42 trs which is required if the sequence data isn't embedded in the gff
21:44 cdiesh trs: oo. ok let me see if thats the case here
21:44 trs I guess it's a behaviour change
21:45 cdiesh trs: ya we don't have the sequence on our gff.
21:45 cdiesh is there any workaround, such as having a sequence file in the same folder, or does it need to be in the gff?
21:47 cdiesh if i read what you said correctly, then I think that a fasta file could simply be in the folder :)? i will test it out
21:47 trs yes
21:55 cdiesh trs: looks like that fixes it!
21:56 cdiesh for real this time. thank you!
22:00 trs cdiesh: the behaviour change happened first in 1.6.910
22:00 trs with this bioperl commit 216622f
22:00 trs which changed the indexer's behaviour from "return unless @files" to "$self->throw(...) unless @files"
22:01 trs "silently don't index anything" to "complain about nothing to index"
22:12 cdiesh ah. well, that error now does make sense :)
22:23 trs glad to help :)
23:30 cdiesh trs: is it ok if i credit you on the jbrowse release notes?
23:31 trs sure
23:33 cdiesh ok thanks again

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