Camelia, the Perl 6 bug

IRC log for #bioperl, 2012-01-17

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All times shown according to UTC.

Time Nick Message
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18:26 ende whats the everyone's latest favorite flavor of blast for searching really short sequences (~30bp tags) ?
19:21 dnewkirk joined #bioperl
19:26 _ilbot joined #bioperl
19:26 Topic for #bioperl is now Be patient!  Sometimes it takes a few minutes for people to notice your question! | http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | nopaste to gist.github.com
19:45 pyrimidine ende: bwa ;)
19:45 pyrimidine though others have used megablast I think
19:47 ende hey thanks
19:47 ende not always up on what the cool kids are using these days ;)
19:54 dnewkirk bwa for what?
20:00 pyrimidine dnewkirk: 12:26 <@ende> whats the everyone's latest favorite flavor of blast for searching really short sequences  (~30bp tags) ?
20:01 pyrimidine my (admittedly smartass answer) was bwa
20:01 dnewkirk ahh
20:01 pyrimidine s/answer\)/\) answer/
20:02 dnewkirk Well, if you have a bit of ram at your disposal and a lot of sequence to align...
20:02 dnewkirk http://nar.oxfordjournals.org/conten​t/early/2011/12/22/nar.gkr1246.full
20:03 pyrimidine huh, may have to check that one out.  We have an SGI with 8TB memory, 384 core
20:05 ende yeah im just tryin to map a bunch of tag profiling tags to unigenes
20:10 * dnewkirk weeps at the thought of having that much computing power at his fingertips
20:12 ende aws
20:15 pyrimidine aws + ngs = $$$
20:16 pyrimidine no one I know has found it to be cost-effective yet
20:16 pyrimidine though we have a lot of resources, so we're a bit spoiled
20:17 dnewkirk aws?
20:21 ende amazon web services
20:21 ende EC2, etc
20:21 dnewkirk ahhh
20:21 dnewkirk sorry
20:37 dnewkirk If Stanford can do Folding@Home, maybe we need some form of distributed sequencing/genome assembly
20:37 dnewkirk :)
20:42 pyrimidine gah, hobbes has no source code!
20:43 pyrimidine bad NAR, bad bad...
20:43 pyrimidine http://hobbes.ics.uci.edu/download.jsp
20:43 pyrimidine precompiled binaries (aka 'I'm too afraid to show my dirty code to the world')
20:45 dnewkirk I can see about getting the source code. I was under the impression they were going to put it up, not sure why they haven't yet...
20:47 pyrimidine just emailed them myself, will hopefully get a response. Surprised this was missed by NAR though
20:47 pyrimidine though SOAP2 went for years w/o a source release
20:48 pyrimidine trying to get hobbes to work on sgi failed with a libbz2 requirement :P
21:04 dnewkirk I had to create some symbolic links in fedora, but it does work.
21:04 dnewkirk Forgot about that.
21:06 dnewkirk If you don't get a response, I can walk down the hall and talk to Alex or Lingjie.
21:10 dnewkirk Er, I can talk to the people who helped write the code that is :)
21:11 pyrimidine dnewkirk: yeah, that might be worth a shot
21:11 pyrimidine I guess ask them whether the source is to be released since the pub is out
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21:24 dnewkirk pyrimidine: it will be released by weeks end
21:25 pyrimidine good to know!  thanks dnewkirk
21:25 ende left #bioperl
21:43 * dnewkirk wonders if the fedora channels are inhabitted by ghosts
21:44 * deafferr1t rattles some chains behind a thin wall
22:00 CIA-3 Bio-EUtilities: Chris Fields master * ra693c64 / (scripts/bp_einfo.pl scripts/Bio-DB-EUtilities/bp_einfo.pl): remove redundant directory - http://git.io/H2W_wg
22:00 CIA-3 Bio-EUtilities: Chris Fields master * raf665e6 / (Changes dist.ini): some cleanup - http://git.io/OT2yDQ
22:03 CIA-3 Bio-EUtilities: Chris Fields master * rb3d48bc / (xt/release/EUtilities.t t/RemoteDB/EUtilities.t): move remote tests over to release testing (these should be run prior to any release, regardless) - http://git.io/KC7oMg
22:03 CIA-3 Bio-EUtilities: Chris Fields master * r11d8653 / xt/release/EUtilities.t : remove Bio::Root::Test, use Test::Most - http://git.io/mVvRGA
22:03 CIA-3 Bio-EUtilities: Chris Fields master * r88699db / xt/release/EUtilities.t : remove extraneous comments - http://git.io/763AqA
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