Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-02-24

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All times shown according to UTC.

Time Nick Message
00:21 driveby_bot joined #bioperl
00:21 driveby_bot /home/svn-repositories/bioperl: r16873 (kortsch) : Follow the bowtie environment variable index location behaviour definition from bowtie manual
00:21 driveby_bot Diff: http://tinyurl.com/yktj3rz
00:36 driveby_bot joined #bioperl
00:36 driveby_bot /home/svn-repositories/bioperl: r16874 (maj) : bug 3015/Emmanuel's fixes for negative cut sites
00:36 driveby_bot Diff: http://tinyurl.com/yj6ahs4
00:37 driveby_bot joined #bioperl
00:37 driveby_bot /home/svn-repositories/bioperl: r16875 (maj) : added Emmanuel's tests for bug3015 patch
00:37 driveby_bot Diff: http://tinyurl.com/ykshblj
00:37 deafferret cut sites??? negative!!
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03:00 driveby_bot /home/svn-repositories/bioperl: r16876 (miraceti) : bugfix provided by Ivica: print bootstrap and branchlength
03:00 driveby_bot Diff: http://tinyurl.com/yzganop
03:03 deafferret Ivica?
03:34 brunov I just realized that your nickname means deaf ferret
03:34 deafferret :)
03:34 brunov how could it take so long? I don't even...
03:35 deafferret only what... 2 years?  :)
03:35 brunov please don't tell my kids
07:33 bag_ joined #bioperl
12:23 huzech joined #bioperl
12:53 faceface rbuels: I missed your reply :(
12:54 brandi joined #bioperl
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14:50 brunov joined #bioperl
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15:37 rbuels faceface: which reply
15:49 faceface don't know
15:49 faceface how are you?
15:49 faceface you said you used mummer to compare very long, very similar sequences?
15:50 faceface should we switch to #gmod for this kind of discussion?
15:58 rbuels well, this is still bioperly
15:58 rbuels faceface: ^^^
15:58 rbuels doing fine.  tons of work.  the scale of my vision is very much at odds with the means at my disposal, lol
16:17 faceface rbuels: yeah
16:17 faceface better than the alternative
16:18 faceface I have a fasta file of 'superscaffolds' and a file of 'scaffolds', and unforutunately no mapping between them
16:18 faceface so I'll use mummer or similar to identify the latter in the former... but its slow
16:19 faceface I figure it is a no brainer because the sequences should be identical
16:19 faceface any hint?
16:19 rbuels no, won't be identical necessary
16:19 rbuels there will be differences in homopolynucleotides ....
16:19 rbuels other basepair changes ...
16:19 rbuels right?
16:19 rbuels or are these actually based on the same assembly
16:21 rbuels i'm surprised mummer is slow in this case
16:21 rbuels is it multithreaded?
16:22 rbuels i mean, it's pushing a hell of a lot of data
16:22 rbuels so i would hope it's multithreaded
16:26 faceface don't know actually
16:27 faceface there may be small diffs... lemmy try finding a few big scaffolds in the superscaffolds
16:27 faceface I have a question about SGN
16:28 faceface who is the target audience?
16:28 rbuels lol, that's a very good question.
16:28 faceface i.e. bioinformaticians, geneticists, molbiols...
16:28 rbuels i don't think anybody knows.
16:28 faceface ;-)
16:28 rbuels what are you getting at?
16:28 faceface OK, who is the audience?
16:28 faceface ;-)
16:28 rbuels all of these people use sgn in one way or another i think
16:28 faceface rbuels: I've been asked to help organize a workshop for 'potato post genome'
16:29 rbuels post genome?
16:29 rbuels oh i get it
16:29 faceface Potato Breeding After the Potato Genome
16:29 rbuels "now that there is a genome"
16:29 faceface Here are the words I have so far...
16:29 rbuels where is this workshop going to be?
16:29 faceface The task breaks down into three roughly sequential parts:
16:29 faceface 1) Assessing the needs of this community w.r.t. accessing the data produced by the PGSC.
16:29 faceface 2) Discovering or creating the data and facilities to meet these needs.
16:29 faceface 3) Organizing a workshop to disseminate the work of step 2.
16:29 rbuels breeders are why we do all this science.
16:29 faceface de netherlands
16:29 rbuels i would dearly like to understand plant breeding better
16:30 faceface rbuels: I think its something to do with birds and bees
16:30 faceface step 2 is where this conversation comes in
16:31 faceface i.e. 'Dear rbuels, what facilities do you have to meet the needs of potato breeders?'
16:31 rbuels answer is: i don't even know what their needs are
16:31 faceface and b) can I steal / hijack them?
16:31 rbuels and i want to know
16:31 faceface right
16:32 faceface so I guess we are both stuck on step 1
16:32 faceface I asked Dan Milbourne to send me a list of 'use case scnarios'
16:32 faceface because my background isn'y breeding either
16:33 rbuels and i don't think you need to steal/hijack them, i'll give you a commit bit on sgn
16:33 faceface perhaps there is a wider rice / wheat / barly community that we can poll
16:33 faceface rbuels: awesome
16:34 rbuels when and where is this workshop, maybe i should go?
16:34 faceface Its 27th - 30th of June
16:34 faceface its a potato breeders 3 yearly meeting
16:35 faceface rbuels: you are now not just attending, your co-chair on a workshop ;-)
16:35 rbuels no i don't think so
16:35 rbuels lol
16:35 faceface seriously though, the informatics side of the PGSC doesn't have much of a 'public facing' interface
16:36 faceface to put it politely
16:36 rbuels that's cause a public facing interface is hard.
16:36 faceface so we need to not only talk about the stuff, we need to develop it first
16:36 rbuels and we need software developers
16:36 faceface right
16:36 faceface unfortunately I am the them
16:36 faceface unfortunately I am the they
16:38 brunov joined #bioperl
16:43 faceface I think mummer may be slow because of sequence repeats
16:44 rbuels sgn labmeeting is going on now
16:44 * faceface disrupts
16:45 faceface stand up and say "I have a brilliant idea"
16:46 rbuels but what do i say after that
16:46 rbuels lol
16:46 faceface say 'my name is rob'
16:46 rbuels they know that.
16:46 faceface tell them that this is your idea
16:46 rbuels lol
16:47 faceface sorry, I'll let you get back to work
16:47 rbuels no this is good
16:47 faceface point them at this structured wiki? http://seqanswers.com/wiki/MUMmer
16:47 rbuels someone from sgn will go to your workshop i think
16:47 faceface cool
16:47 rbuels go to #cxgn and talk to lukas
16:47 faceface which server?
16:47 rbuels irc.perl.org
17:18 deafferret o..
17:27 rbuels ..@:.
17:52 pyrimidine joined #bioperl
19:22 pyrimidine left #bioperl
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20:56 pyrimidine *** crickets ***
20:57 * deafferret drools
20:57 * deafferret lools
20:57 * pyrimidine spools
20:57 * deafferret falls off his chair.    twice.    but we can't remember why.
20:58 * deafferret goes loco with the cake
20:58 * deafferret runs out of #bioperl memes  (#rbuels-silliness)
20:58 * pyrimidine wonders where rbuels is
20:58 deafferret phant: remind me of more memes!
20:58 deafferret bots: seen rbuels?
20:58 rbuels oh i'm around
20:58 * deafferret lools
20:58 pyrimidine just ignoring the noise, I see
20:59 deafferret rbuels: does this highlight your window?
20:59 * pyrimidine stomps off and pouts in a corner
20:59 rbuels deafferret:  yes it does, as you well know
20:59 deafferret rbuels: ok. thanks. I won't bug you then.
20:59 rbuels :-p
20:59 rbuels hehe
20:59 pyrimidine rbuels rbuels rbuels
20:59 * deafferret sets up a clock-watch rbuels alert
20:59 rbuels deafferret:  aw, there's no hard feelins little buddy
20:59 * rbuels ruffles deafferret's hair
21:00 * pyrimidine wishes he had hair to ruffle
21:01 * deafferret clutches rbuels to his man-boobs, weeps
21:02 rbuels deafferret: you need something to do?  add a queue_size method to moosex::workeres
21:03 deafferret weird... I don't see an rt.cpan.org ticket for that
21:03 rbuels deafferret: and while you're in there, see if you can figure out why millions of things in the queue slows it down
21:03 rbuels oh hell
21:03 deafferret rbuels: you're in line behind pmooney patches this morning
21:03 rbuels pmooney?
21:03 deafferret sudo rbuels /me takes a number
21:03 deafferret github fork
21:04 deafferret added TERM handling. woot!
21:04 deafferret that's the rumor anyway, haven't gotten to it yet
21:04 rbuels theres a new tomato genome release targeted for friday
21:04 rbuels going through and making sure all the stuff is ready for it
21:05 deafferret ! $tomato @ISA qw( fucker )   ?
21:05 rbuels is that .... perl?
21:05 deafferret perl 5.11.2 is the shiznit
21:06 rbuels surely that was not valid perl syntax
21:09 deafferret joined #bioperl
21:09 * deafferret feeds the phant
21:10 was kicked by shirly: NO FERRETS!
21:11 deafferret joined #bioperl
21:11 deafferret woo woo wooo
21:11 shirly hmm
21:11 deafferret shirly?  who the hell is shirly?
21:11 shirly oh dear. I need k-line to get my nick back
21:12 deafferret shirly, what nick?
21:12 deafferret deaferferret: can't you think of a better name than that?
21:12 deafferret people might confuse you with me.
21:13 was kicked by deaferferret: I feel so helpless! sob!
21:13 deafferret joined #bioperl
21:13 * deafferret capers about
21:13 deafferret look at me, my name's deaferferret
21:13 deafferret er...
21:13 deafferret deafferret
21:13 * deaferferret lools
21:15 rbuels hmm, should i wait ....
21:15 was kicked by deaferferret: wait over there
21:15 was kicked by deaferferret: with him
21:16 deafferret joined #bioperl
21:16 rbuels joined #bioperl
21:16 rbuels no, i think i'll wait over here
21:16 deafferret yeah, me too
21:16 * deaferferret screams
21:16 * pyrimidine snores
21:17 * deaferferret starts Grey Gardens documentary on infinite loop to calm himself
21:17 rbuels yeah i'm starting to get bored of this though
21:17 rbuels provides on opportunity to compare xchat and konversation side by side though
21:17 deafferret too bad i have to use this dumb nick with xchat
21:18 deafferret oooo, xchat can detach channels
21:19 deafferret i think i might like it better
21:20 brunov LOOK! A DEAF FERRET!
21:20 deaferferret DEAFer
21:21 * deaferferret didn't hear you anyway
21:21 brunov I'm stoked. I see everything in a new light now.
21:22 rbuels brunov: why?
21:22 brunov just yesterday I realized that deafferret means "deaf ferret"
21:22 brunov I feel like Neo in the Matrix
21:22 rbuels lol
21:23 brunov I can see through the 1337
21:23 rbuels deaferferret: better /nick, or i'll take it again
21:23 rbuels lol
21:23 * deaferferret kinda likes this one, updates the wiki
21:23 deaferferret guess I'll have to go back to NickServ identify on next reboot
21:23 deaferferret then grab this one back again
21:24 deaferferret coming soon: deafestferret
21:24 brunov see? I got that one too!
21:24 * deaferferret assumes this nick is even more brunov-confusing, which is a plus
21:25 pyrimidine deafandmuteandblindferret?
21:25 brunov deaferferret, I'm immune to your powers now
21:25 deaferferret :(
21:25 deaferferret /kick brunov immunity test
21:25 brunov see? I wonder... I wonder If I could fly
21:25 * brunov tries
21:26 deaferferret ow
21:26 deaferferret sudo rbuels /me cleans up that mess
21:26 brunov joined #bioperl
21:26 brunov nope
21:27 * deaferferret grovels before his risen lord and saviour
22:58 brunov joined #bioperl
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