Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-07-24

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All times shown according to UTC.

Time Nick Message
00:01 carandraug joined #bioperl
02:48 CIA-94 joined #bioperl
06:30 pierre_ joined #bioperl
06:31 pierre_ can anyone here help with some github questions?
06:55 bag_ joined #bioperl
07:20 dnewkirk_home joined #bioperl
09:05 bag_ joined #bioperl
14:54 ank joined #bioperl
15:41 deafferret .o.ooo.
16:26 dnewkirk_home good morning
16:30 * deafferret waves
16:32 dbolser morning
16:34 deafferret ooo! Saturday morning party!
16:36 * dbolser gets beer
16:45 deafferret lol...   "Don't sweat the petty things. Don't pet the sweaty things either."
16:49 dbolser deafferret: so I'm now working on the bioperl codebase from home... I first hit "git add" then "git commit then git push dbolser at work, then at home I'm git clone'ing dbolser
16:49 dbolser deafferret: so I'm now working on the bioperl codebase from home... I first hit "git add" then "git commit" then "git push dbolser" at work, then at home I'm "git clone dbolser"'ing
16:49 dbolser does that sound about right?
16:49 deafferret you only clone once.  after that you pull
16:50 deafferret so if you don't have the code at home AT ALL, yes, clone
16:50 dbolser ok, right, cool
16:50 deafferret once, then pull for the next several years
16:50 deafferret until we switch to newfangledvcthing
16:50 dbolser I do have bp, but aparently not live
16:50 dbolser right....
16:50 deafferret they make a bioperl-notlive?   why would anyone want THAT?  :)
16:50 dbolser when's that then?
16:51 dbolser right, it's called 'bioperl dead-donky'
16:51 dbolser you "git flog dead-donkey"
16:51 deafferret oh, who knows. it'll probably be called youregettingold
16:51 deafferret youregettingold clone oldie:oldhub.com/bioperl-live.git
16:52 dbolser ur-too-old merge hyperbrain
16:52 deafferret err...   gitoffmylawn
16:52 deafferret :)
16:52 dbolser git clone is killing my network so perhaps see you later
16:52 deafferret "grandpa, you're still on 'The Internet'??"
16:52 deafferret really? shouldn't
16:53 deafferret hmm... bioperl-live is 195MB
16:53 deafferret dunno if git clone compresses over the wire
16:58 dbolser bad wifi
17:00 dbolser greatgrandpa, you remember a time before perl 6!
17:09 dbolser how do I 'reconfigure' my urllist in cpan?
17:15 dbolser o conf init urllist :-D
17:18 deafferret :)
18:39 dbolser WARNING: the following files are missing in your kit: t/Assembly/10_core.t t/Assembly/20_bowtie.t t/Assembly/30_sam.t
18:39 dbolser Please inform the author.
19:17 dbolser is there a bio::assembly::Gap object?
19:19 dbolser does an assembly::scaffold check it's contigs have unique ids?
19:20 _ilbot2 joined #bioperl
19:20 Topic for #bioperlis now http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | paste to http://pastebin.com/
19:31 bag_ joined #bioperl
19:32 dbolser what is the right way to locate a contig in a scaffold?
19:32 dbolser i.e. when building a contig (or a scaff) how is that data stored?
19:45 dbolser I'm totally confused about how to represent assemblies in bp
20:00 dbolser how do i run a test?
20:01 dbolser got it
21:12 _ilbot2 joined #bioperl
21:12 Topic for #bioperlis now http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | paste to http://pastebin.com/
22:29 dbolser what determines the perms of installed files?#
22:30 dbolser -r--r--r-- 1 dmb dmb 37579 2010-07-24 19:48 ace.pm
22:30 dbolser -r--r--r-- 1 dmb dmb  8693 2010-07-24 23:27 agp.pm
22:30 dbolser -r-xr-xr-x 1 dmb dmb  9422 2010-07-24 19:48 bowtie.pm
22:30 dbolser -r-xr-xr-x 1 dmb dmb 17721 2010-07-24 19:48 maq.pm
22:30 dbolser -r--r--r-- 1 dmb dmb 14666 2010-07-24 19:48 phrap.pm
22:30 dbolser -r-xr-xr-x 1 dmb dmb 21843 2010-07-24 19:48 sam.pm
22:30 dbolser -r--r--r-- 1 dmb dmb 51886 2010-07-24 19:48 tigr.pm
22:30 dbolser wah?
22:51 deafferret ?
22:52 deafferret installed how?
22:52 deafferret regardless, I don't know
22:54 dnewkirk I would imagine that is set by the person to last add/change code to any of the modules...
22:55 dnewkirk github doesn't adjust the file permissions as far as I'm aware
23:16 dbolser well.. installed files are ro
23:16 dbolser but the co gives me rw files
23:16 dbolser ./Build install
23:16 dbolser so... anyone familiar with Scaffold and Contig objects?
23:17 dbolser because... I'm creating contigs in the 'next_contig' method - this method actually reads and parses the file
23:17 dbolser however, the 'next_assembly' method sticks the contigs into a scaffold object
23:18 dbolser and I'm wondering, how to set the id of the 'outer' scaffold object based on data that is being read by the contigs.
23:19 dbolser like... should I give the contigs a scaffold somehow? and how is this affected by giving the scaffold the contig... (if that makes sense).
23:22 * dbolser looks at line 199 of ace.pm
23:24 deafferret sorry, don't know squat about assemblies
23:24 deafferret I'd like to, but I don't see that in my near future
23:25 dbolser deafferret: it looks complex
23:25 dbolser I need to see some nice overview diagram
23:25 * dbolser assumes there is no assembly HOWTO
23:26 deafferret not that i've seen. it seems hard to pin down, even amongst people who do it for a living
23:27 dbolser deafferret: how would you feel about helping to write a bp book?
23:27 deafferret uh, i just started my own consulting business, so I doubt I'll have time for that for a couple years
23:28 dbolser ic
23:28 deafferret not sure I have enough patience to write a whole book, given limited payment to do it
23:28 dbolser deafferret: the payment comes later ;-)
23:29 deafferret ya, i'm guessing it's not tons of money though, and short shelf life in biotech ?
23:29 deafferret obviously, I know nothing about authoring  :)
23:29 dbolser ne 'never
23:29 dbolser me ne'ver
23:30 dbolser so far I have determined the following...
23:30 dbolser an assembly is a big ball of different sequence and feature objects.
23:30 dbolser with some random methods thrown in
23:31 * dbolser fictionally turns to the assembly chapter in his fictional 'essential bp' book
23:32 dbolser s/assembly chapter/fictional assembly chapter/

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