Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-04-08

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All times shown according to UTC.

Time Nick Message
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07:54 dbolser example of Pod::Usage?
08:05 dbolser nm, got what I wanted here: https://github.com/bioperl/bioperl​-live/pull/11#issuecomment-971324
08:05 dbolser silly 'priority inbox' doesn't recognize my interests
08:12 dbolser yay for bug #3110!
08:12 dbolser thanks Chris
09:48 buelsbot left #bioperl
09:48 dbolser another day another $_
09:48 dbolser Can't locate object method "update" via package "Bio::DB::SeqFeature::Store::DBI::mysql" at ./patch_db_sfs.plx line 24.
09:50 dbolser http://search.cpan.org/~cjfields/BioPerl-1​.6.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm # documented here no less
09:51 dbolser here's mah script: https://gist.github.com/909576
09:53 * dbolser updates his GFF instead
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15:44 dbolser if I put landmarks and landmark fasta in one SeqFeature::Store::mysql, and other features in another, is it a big problem?
15:44 dbolser can I get the sequence of those other features?
15:44 dbolser I'm starting to get confused by the combinatorial challenge of managing n gff files in y sfs dbs
15:47 rbuels dbolser: i don't see how it would be a 'big problem', but then i've never tried it
15:54 dbolser I'll just reorganize my GFF folder and hope my pipelines follow
16:07 rbuels haha, ok
16:07 dbolser I guess 5pm on friday is as good as time as any...
16:08 rbuels 5pm on friday is also the best time for merging a big branch
16:08 rbuels (if you're using a version control system that can merge)
16:08 rbuels (i.e. not svn)
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18:00 * dbolser merges with the hive mind
18:01 rbuels wow, no resistance at all
18:02 rbuels would have been futile anyway
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18:34 pyrimidine dbolser: I have a specific database that houses features I want to keep around or I don't expect to change (gene models and FASTA)
18:34 pyrimidine dbolser: and keep other stuff, such as analysis results, in another db,
18:35 pyrimidine never had much of a problem.  Only works with GBrowse2 well, though
18:36 dbolser pyrimidine: ic
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18:38 dbolser pyrimidine: do you know about the lack of 'update' in db:sfs:mysql.pl
18:39 dbolser https://gist.github.com/909576
18:40 pyrimidine dbolser: update() is a feature method
18:40 pyrimidine $f->update()
18:41 dbolser pyrimidine: oh.. docs fail
18:41 pyrimidine if you want to update using the store, I think that is '$store->store($f)'
18:41 pyrimidine or something like that
18:42 pyrimidine dbolser: the docs still wrong?  I thought this was fixed....
18:42 * pyrimidine will check in just a sec...
18:42 dbolser http://search.cpan.org/~cjfields/BioPerl-1​.6.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm
19:04 pyrimidine dbolser: I meant in github
19:10 dbolser oic
19:11 dbolser shame latest pod isn't in wiki... (like I said it shouldn't be)
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19:42 * dbolser discovers everyones dark secrets http://www.kgbpeople.com/
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19:45 dbolser Netlog is the online community for more than 75 million young people.
19:45 dbolser wut?
19:47 rbuels o_O
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20:07 rbuels pyrimidine:  http://sgn-devel.sgn.cornell.edu:8080/tools​/blast/show_match_seq.pl?blast_db_id=139;id​=SL2.31ch03;hilite_coords=64840951-64840952
20:08 rbuels pyrimidine: this is an illustration of why bioperl's hacked-up homebrewed backtracing stuff is the suck.
20:08 rbuels pyrimidine: this die actually happened in a mason component
20:08 rbuels pyrimidine: but you can't tell what line
20:08 rbuels eh, well actually you can
20:08 * rbuels chuckles
20:09 pyrimidine rbuels: that's purty
20:09 rbuels it's a port forward to my dev machine
20:09 * rbuels takes it down
20:10 rbuels pyrimidine: actually, if you do web dev, this is pretty useful
20:10 rbuels pyrimidine: https://github.com/solgenomics/sgn​-devtools/blob/master/dev_gateway
20:10 rbuels pyrimidine: just have a machine with a range of ports open, but nothing running on them
20:11 rbuels pyrimidine: and then when you want to show somebody someplace your dev server, this script will calculate and run the necessary port forward for you
20:11 * rbuels ran dev_gateway -p 3000 sgn-devel.sgn.cornell.edu
20:11 pyrimidine slick!
20:11 rbuels to forward my cat dev server.
20:11 rbuels pyrimidine: looks like this https://gist.github.com/910607
20:13 pyrimidine so, basically a nice, easy-to-close temporary window to your dev server
20:14 rbuels yep
20:14 * pyrimidine marks that link
20:14 rbuels supports multiple users for one gateway box
20:15 rbuels this one has the gateway ports hardcoded at 8080..8090
20:15 rbuels so many users in a group can use that.
20:15 rbuels chris runs it, and will get 8080.  alice will get 8081, bob will get 8082, etc.
20:57 CIA-119 bioperl-live: Scott Cain master * r3a73b74 / t/LocalDB/BioDBGFF.t : removed a few tests that can return ambigous results depending on a sort - http://bit.ly/h7wiHO
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