Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-06-18

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All times shown according to UTC.

Time Nick Message
01:11 brandi joined #bioperl
01:11 brandi left #bioperl
04:28 nuba left #bioperl
04:37 dnewkirk_ 17 hours to build an index? What organism? I can build it in an hour likely on my machine here if you wish...
04:57 CIA-52 biome: Chris Fields master * r5cfc368 / (12 files in 5 dirs): split IO up into roles, add tests (still a few mroe things to do) - http://bit.ly/a3jo5E
04:58 CIA-52 biome: Chris Fields master * r2a92909 / t/Role/IO.t : updates to tests - http://bit.ly/bN4wTs
04:59 CIA-52 biome: Chris Fields master * raa3ad7a / MANIFEST : update MANIFEST - http://bit.ly/aZrBoD
05:33 flu joined #bioperl
05:55 CIA-52 bioperl-live: Florent Angly master * r85bdf82 / Changes :
05:55 CIA-52 bioperl-live: Updated 'Changes' file regarding assembly improvements since
05:55 CIA-52 bioperl-live: bioperl-live v1.6.1 - http://bit.ly/bzz9tx
06:21 CIA-52 bioperl-run: Florent Angly master * rd7fea48 / Changes : Updated 'Changes' files for new assembly-related additions since v1.6.1 - http://bit.ly/adRqTC
06:38 vinnana joined #bioperl
07:04 CIA-52 bioperl-run: Florent Angly master * rb916172 / (3 files in 2 dirs):
07:04 CIA-52 bioperl-run: Support for assembly variants in Bio::Tools::Run::AssemblerBase
07:04 CIA-52 bioperl-run: Bio::Tools::Run::Newbler fixed to output ACE-454 variant - http://bit.ly/cCqdvY
11:33 kai hm, this is off-topic, but what do you people use to create publication-quality alignments? I used something for my thesis, but can't even remember what it was called
12:09 brandi joined #bioperl
12:11 brandi left #bioperl
13:55 CIA-52 biome: Chris Fields master * rdd3b4ff / (7 files in 5 dirs): POC for SeqIO, with very minimal tests for runtime role application - http://bit.ly/9keKEy
14:42 faceface kai: jalview is developed 3 m from me
14:42 faceface and its good at that
14:58 Jun yep, jalview is good. Or bioeditor
14:58 Jun Or seaview
14:59 Jun Plus there is a new BioPerl package called Bio::Align::Graphics, you may consider to try it
15:01 Jun And, for me, I will just printscreen of the text of .aln alignment. It is good enough for me. Easy and clear...
15:07 kblin I use jalview as well, but that doesn't line-break alignments so they'll fit on a page, right?
15:31 faceface not sure
17:47 deafferret .:.
17:48 deafferret spekki0: did you figure that out?
17:48 deafferret dnewkirk: 17 hours to build hg19 on an 8 CPU 32GB RAM box
17:54 spekki0 oh hey
17:55 spekki0 yeah i figured out my error
17:55 spekki0 it was just ncbi's servers acting up cause after a couple re runs of the code it worked
17:55 deafferret :/
18:09 rbuels ncbi's servers act up fairly frequently.
18:16 pyrimidine joined #bioperl
18:19 deafferret rbuels: shh! you awakened the pyrimidine
18:19 deafferret the fearsome py[TAB]!
18:19 rbuels pytab!
18:20 * rbuels hides in the undergrowth
18:20 * rbuels chuckles
18:20 py[tab] even better
18:20 deafferret hmm, my keyboards says Tab\n|<--\n-->|
18:21 deafferret pro tip: the singular of keyboards is keyboards
18:21 rbuels o_O
18:22 deafferret don't you woggle your cartoony eyeballs at me mister
18:23 py[tab] .o0
18:26 py[tab] Anyone ever use IO::Unread?
18:27 * deafferret offers a zany undead joke
18:27 * deafferret basks in the thunderous laughter
18:28 * py[tab] scared of thunder
18:29 py[tab] deafferret: didn't know you played harmonica
18:29 deafferret py[tab]: I'll have plenty of time to learn
18:30 py[tab] :)
18:30 deafferret py[tab]: so, what's YOUR excuse for ditching me at YAPC?  jerk.
18:30 py[tab] re: YAPC, Scott Cain might be there (he's in the area).  Also, Genentech is sponsoring, so George Hartzell is going
18:30 deafferret oh? cool. haven't seen Scott in ~3 years
18:31 py[tab] my excuse?  still waiting to see if I'm moving or staying, etc
18:31 deafferret is George a bioperl guy?
18:31 py[tab] yes
18:41 CIA-52 biome: Chris Fields master * r05e30d3 / (4 files in 4 dirs): small updates to SeqIO - http://bit.ly/djOnlG
18:42 rbuels wow, genentech is sponsoring??
18:42 * rbuels feels proud
18:42 rbuels i told <yapc guy> to contact them
18:42 py[tab] :)
18:42 rbuels and george
18:43 rbuels i'm not going because i am a weenie
18:43 rbuels and also because my june has been EFFING CRAZY
18:43 py[tab] I would like to go, just really bad timing
19:17 pyrimidine left #bioperl
19:17 * deafferret sniffs
19:26 CIA-52 biome: Chris Fields master * r93f8e5e / (4 files in 4 dirs): Merge branch 'master' of git@github.com:cjfields/biome - http://bit.ly/d66Yb7
19:26 CIA-52 biome: Chris Fields master * r7de1bc4 / (4 files in 4 dirs): issue with inheritance and runtime roles, needs looking into - http://bit.ly/bfBqiE
19:34 deafferret (Merge branch 'master')++
19:48 * rbuels chuckles
19:51 * deafferret shucks Ls
20:40 CIA-52 biome: Chris Fields master * r484446f / (lib/Biome/SeqIO.pm t/SeqIO.t): does help to use Biome instead of Bio...grr.... - http://bit.ly/bAZFfe
20:41 deafferret Bio...grr....: not found
20:41 deafferret BioGrl?
20:41 deafferret save us!

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