Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-08-05

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All times shown according to UTC.

Time Nick Message
02:44 CIA-72 bioperl-live: Chris Fields topic/most_testiest * r116b84d / (20 files in 7 dirs): remove lib files (not sure about Error.pm yet) - http://bit.ly/qo4a3h
03:52 CIA-72 bioperl-live: Chris Fields topic/most_testiest * r8b6e449 / Build.PL : bbuild_requires Test::Most - http://bit.ly/oqZw4L
03:52 CIA-72 bioperl-live: Chris Fields topic/most_testiest * rf2c3234 / Bio/Root/Test.pm : get tests working from Test::Most; need to evaulate use of Bio::Root::Test::Warn, but tests are passing now - http://bit.ly/rqy7NH
03:52 CIA-72 bioperl-live: Chris Fields topic/most_testiest * rc0b01f8 / Bio/Root/Test.pm : use @EXPORT from Test::Most (which does the hard work) - http://bit.ly/oOV9Dc
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14:34 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
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18:17 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
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18:51 jessicajames I'm trying to run blast from within a perl script and I keep getting this error (MSG: cannot find path to blastall)
18:52 jessicajames I have BLAST installed, and "perl -e 'print $ENV{PATH}, "\n"'" contains /usr/bin which is where the blast executables are located
18:52 jessicajames Can anyone help me with this issue?
18:52 rbuels hmm
18:53 rbuels jessicajames: if you type 'blastall' at the command line, does it run?
18:53 rbuels jessicajames: i.e. do you get its help output?
18:54 jessicajames blastall isn't found, but the following are found: blastdb_aliastool  blastdbcmd         blastn             blastx blastdbcheck       blast_formatter    blastp
18:54 rbuels jessicajames: well, that means you don't have blastall installed
18:54 rbuels jessicajames: or at least it's not where you think it is
18:55 rbuels jessicajames: if you're using ubuntu, it should be in /usr/bin/blastall
18:55 rbuels jessicajames: the ubuntu package for it is 'blast2'
18:55 jessicajames i'm in fedora, i'll look in the repositories for it
18:57 jessicajames can't find it..
18:58 jessicajames okay
18:59 jessicajames i just downloaded it from ncbi's site - i'll uninstall fedora's version and install ncbi's
18:59 jessicajames it seems to contain blastall
19:02 rbuels jessicajames: so, once you install that, you should be able to type blastall  and see its help output come up
19:03 jhannah so violent. you don't have to blast *everything*
19:03 jessicajames okay
19:03 * rbuels calls for his elephant gun
19:03 jessicajames now when i type 'blastall' i get 'blastall 2.2.25   arguments:'
19:03 jessicajames and a list of arguments
19:03 rbuels jessicajames: yep, so now i bet your script will be able to find it
19:04 jessicajames yup :)
19:04 jessicajames thanks
19:05 rbuels np
19:05 rbuels consider donating to the RIDB
19:05 * rbuels chuckles
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19:07 jessicajames what's the RIDB?
19:08 rbuels jhannah: aren't you going to explain?  you're the executive vice president, after all
19:09 rbuels jessicajames: it's the Rbuels Institute for Distraction in Bioinformatics.  just a running joke.  ignore.
19:09 rbuels heh
19:09 jessicajames lol
19:10 jhannah jessicajames: rbuels does not have the authority to demean the monumental importance of the RIDB. He will be dealt with accordingly.
19:10 rbuels yeah, my position is largely symbolic
19:10 rbuels i'm kind of a figurehead
19:11 rbuels like queen elizabeth
19:11 jhannah like the English royal family, but with a budget of $0
19:11 jhannah (which is still excessive)
19:11 * rbuels is his own royal family
19:12 jhannah /me is an alias to /we
19:12 jhannah if you are rbuels
19:12 jhannah this is rbuels' cue to say 'we are not amused'
19:12 jhannah but he is distracted.  RIDB++
19:13 rbuels eh?  what?
19:13 rbuels oh
19:13 jhannah distracted from his distractions. he's THAT good
19:14 * rbuels hopes jessicajames is not still reading this BS
19:14 jessicajames no i left
19:14 jessicajames lol
19:14 rbuels good
19:14 CIA-72 bioperl-live: Chris Fields topic/most_testiest * rac1c457 / (Bio/Root/Test.pm Bio/Root/Test/Warn.pm): moved Test::Warn-related hacks to Bio::Root::Test, no need for Bio::Root::Test::Warn - http://bit.ly/qIF6nh
19:15 rbuels was kicked by deafferret: BS this, buster
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19:16 rbuels agh, don't do that while i'm distracted
19:16 deafferret heehee turkeyberry
19:16 rbuels was kicked by deafferret: implying that a lack of distraction would ever exist
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19:16 * rbuels is cowed
19:16 deafferret sorry, RIDB regulations
19:16 deafferret very strict
19:16 * rbuels nods sagely
19:17 * deafferret lools
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19:19 deafferret ah, the RIDB grows strong this day
19:20 dnewkirk RIDB?
19:20 * dnewkirk wonders if he should ask
19:20 deafferret Rbuels' Institute for Distraction in Bioinformatics
19:20 deafferret Rbuels' Institute for Distraction in Bioinfo--SQUIRREL!
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19:24 CIA-72 bioperl-live: Chris Fields topic/most_testiest * r0468502 / Bio/Root/Test.pm : a little cleaning up - http://bit.ly/r0I0nt
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20:43 CIA-72 bioperl-live: Chris Fields master * rbb7ddf4 / Bio/Root/Test.pm : a little cleaning up (+5 more commits...) - http://bit.ly/p1qhQm
20:55 CIA-72 bioperl-live: Chris Fields master * r3823b70 / Bio/LiveSeq/SeqI.pm : use eq, not == for string comparisons; fixes bug#3257; thanks to sixela De bourgogne - http://bit.ly/oiW3Ey
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22:32 CIA-72 bioperl-live: Kai Blin master * r0a9f05b / (Bio/Root/IO.pm t/Root/RootIO.t):
22:32 CIA-72 bioperl-live: Root::IO: Make the readbuffer a stack, not a FIFO
22:32 CIA-72 bioperl-live: Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de> - http://bit.ly/opgXxs
22:32 CIA-72 bioperl-live: Kai Blin master * r3d32a72 / (4 files in 2 dirs):
22:32 CIA-72 bioperl-live: SearchIO::hmmer: correctly handle format determination on non-seekable filehandles
22:32 CIA-72 bioperl-live: This fixes bug #3264.
22:32 CIA-72 bioperl-live: Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de> - http://bit.ly/pfqIAt
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23:29 * rbuels is feeling so fly, like a G6
23:48 deafferret http://www.youtube.com/watc​h?v=w4s6H4ku6ZY&amp;ob=av3e

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