Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-07-08

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All times shown according to UTC.

Time Nick Message
04:53 faceface joined #bioperl
05:14 luisrodr joined #bioperl
10:28 Jun joined #bioperl
11:10 faceface anyone alive?
11:11 faceface Bio::DB::SeqFeature::Store->new( ... -namespace = 'foo' ...)
11:11 faceface Bio::DB::SeqFeature::Store::GFF3Loader->new( the connection ) ...
11:11 faceface can't find table 'feature'
11:11 faceface should look for foo_feature
11:11 faceface I seem to remember debugging this previously
11:13 faceface yeah, found the bug
11:14 faceface table name is hardcoded in Bio/DB/SeqFeature/Store/DBI/mysql.pm
12:49 brandi joined #bioperl
13:15 brandi left #bioperl
13:31 faceface where is the bug tracker?
13:32 brandi joined #bioperl
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13:33 faceface /topic http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | http://bugzilla.bioperl.org/
13:34 * faceface indeafferently points at deafferret
13:58 brandi joined #bioperl
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15:10 rbuels faceface: i would recommend against maintaining your own forked copy of bioperl
15:10 rbuels faceface: but if you want to do it, definitely git is the way to go.
15:11 faceface rbuels: just wondering if it was a good way to report patches
15:11 faceface then (from what I heard) devs can pull my copy and push it onto origin
15:12 rbuels faceface: i probably should have used a term other than forked
15:13 rbuels faceface: i guess what i'm saying is that if there is some kind of functionality that you need to change, it's a pain to keep that around and never merge it into vanilla bioperl
15:14 rbuels faceface: but for bugfixes and stuff, yes, fork it on github and do the fixes there
15:14 rbuels faceface: and then a core dev can pull it, review it, and push it to the main bioperl repo
15:15 faceface cool
15:16 faceface rbuels: I don't suppose you could add instructions on how to do that here: http://www.bioperl.org/wiki/Using_Git
15:17 faceface also, since you're a git guru, I made some minor changes to teh text there to make it easier to understand, but may be incorrect
15:18 faceface http://www.bioperl.org/w/index.php?title=​Using_Git&diff=13397&oldid=13380
15:18 rbuels hmm
15:19 faceface sorry
15:19 rbuels faceface: yeah i think those are right
15:20 faceface :D
15:20 rbuels faceface: thanks for adding those links
15:20 rbuels faceface: i'm pretty swamped right now, i can't really work on the git instructions,
15:20 rbuels faceface: but if you make more improvements i can review them
15:20 faceface np, I'll try to work out what is needed
15:21 rbuels faceface: with a similar diff link process
15:21 faceface ty
15:21 faceface have a good day
15:21 * rbuels thinks this is unlikely
15:21 rbuels lol
15:21 rbuels (the good day part i mean)
15:21 faceface have a day ;-)
15:21 rbuels things are getting crazy in tomato land, as i am sure they are in potato
15:29 faceface heh
15:29 * faceface makes a verbal agreement
16:00 faceface any bioperl list moderators here?
16:00 faceface The reason it is being held: Message has a suspicious header
16:00 faceface what can I say? if "kill all python programmers"  is suspicious, then I'm guilyt
16:06 rbuels god i hate the open-bio mail server config
16:06 rbuels it's so frickin paranoid it's nearly useless
16:34 CIA-95 bioperl-live: Lincoln Stein master * r3f8e736 / Bio/DB/SeqFeature/Store/DBI/mysql.pm : added Dan Bolser's patches to fix inconsistent namespacing issues in the mysql adaptor - http://bit.ly/aGwDQx
16:34 CIA-95 bioperl-live: Lincoln Stein master * r111994e / Bio/Location/Simple.pm : Merge branch 'master' of github.com:bioperl/bioperl-live - http://bit.ly/cAnf5u
16:40 faceface Can't create '/local/Scratch/dbolser/perl5/bin' <- why are you trying to do that dave?
16:41 faceface bioperl install
16:41 faceface grep -r Scratch ~/.cpan/* # Binary file /homes/dbolser/.cpan/Metadata matches
16:52 CIA-95 biome: Chris Fields master * r37de31d / Build.PL : add IO::Unread, unadd(?) MooseX::Singleton - http://bit.ly/bkgKNE
17:52 faceface why does gbrowse have a special behaviour reserved just for me?
18:29 CIA-95 bioperl-live: DaveMessina master * rfb81d7b / (Bio/Annotation/DBLink.pm Bio/SeqIO/seqxml.pm): adding optional -type parameter (and support for it in SeqIO::seqxml - http://bit.ly/aX45OC
18:30 faceface can someone point me at a step by step guide to adding a new datasource / database?
18:30 rbuels faceface: in gbrowse?
18:32 rbuels faceface: you probably want http://gmod.svn.sourceforge.net/vi​ewvc/gmod/Generic-Genome-Browser/t​runk/htdocs/tutorial/tutorial.html
18:32 rbuels faceface: if you are using the 2.x gbrowse.  which you probably are.
18:32 rbuels faceface: but also, this question is kind of for #gmod ...
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20:17 CIA-95 bioperl-live: Scott Cain master * rcb475a3 / scripts/bioperl_netinstall.pl :
20:17 CIA-95 bioperl-live: adding a bioperl commandline netinstaller based on the gbrowse
20:17 CIA-95 bioperl-live: netinstaller. Tested on Mac OS X 10.5, a recent Debian and
20:17 CIA-95 bioperl-live: WinXP. - http://bit.ly/bIBMvG
20:17 CIA-95 bioperl-live: Scott Cain master * rcc09af2 / (112 files in 47 dirs): Merge branch 'master' of github.com:bioperl/bioperl-live - http://bit.ly/biO6of
20:18 bag joined #bioperl
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23:25 ende joined #bioperl

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