Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-11-01

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All times shown according to UTC.

Time Nick Message
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09:05 dbolser doctor.md?
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15:36 deafferret ...oo0o__00
15:36 dbolser deafferret: do you know your place in the universe?
15:37 dbolser http://primaxstudio.com/stuff/scale_of_universe/
15:37 * rbuels chuckles
15:37 dbolser hi rbuels
15:37 * rbuels waves
15:37 deafferret dbolser: self-doubt and loathing?
15:38 deafferret oh wow! that's cool
15:38 dbolser :D
15:39 dbolser not sure how we can add 'the internet'
15:39 deafferret the moon is roughly the same width as the continental US -- neato
15:41 deafferret oh!! flipping cool
15:41 rbuels wow, this thing is cool
15:41 rbuels i hope all this info is correct
15:41 deafferret 7m giant earthworm? really??
15:42 deafferret "large beach ball"   "small beach ball"  lol
15:42 rbuels deafferret: come on man, i'm already all the way to Regulus
15:42 deafferret PS -- I'm MUCH bigger than the "Human" they list there
15:42 rbuels lol
15:42 dbolser would be good to be able to add things
15:42 deafferret lol
15:42 rbuels oh, that would be so awesome
15:42 deafferret "Human"    "Jay"
15:42 * dbolser spaces out
15:43 dbolser actually, I wonder what this is like on lsd
15:43 rbuels all you'd need would be a picture and a size, and then you could have an algorithm to place them
15:43 rbuels and you'd need to write a web interface to review them
15:43 rbuels but that's pretty easy....
15:44 rbuels wow, the pillars of creation is only 10 light-years away?
15:45 * rbuels will go there in cold-sleep after he has outlived all his friends
15:45 deafferret Quantum foam?? wha?
15:45 deafferret "any length shorter makes 'no physical sense'"   hahahaha
15:46 dbolser rbuels: http://www.bbc.co.uk/worldservice/docume​ntaries/2010/10/101027_eatf_kenyon.shtml
15:46 dbolser meh, I've seen smaller
15:47 * rbuels will henceforth give all length estimates in yottameters
15:50 deafferret weak. yoctometers ftw
15:54 deafferret hmm... computer pixels are 0.3mm? seems pretty big to me?
15:58 deafferret huh. 0.23mm on my Macbook. very well.  :)
16:18 rbuels lol
16:19 deafferret the dotpitch of that lol is 2.65mm
16:44 dbolser l00l
17:00 svaksha left #bioperl
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17:06 dbolser hi
17:07 dbolser how do I get a list of every position with depth > n from a sorted bam file?
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17:14 deafferret dunno what a bam file is. is there an IO module for that?
17:19 dbolser prolly
17:20 dbolser http://search.cpan.org/~lds/B​io-SamTools/lib/Bio/DB/Sam.pm
17:21 dbolser just installing the latest version of sam, ncurses-devel, purl-ncurses
17:39 dbolser is there some trick to installing bio::sam
17:43 dbolser ---- Unsatisfied dependencies detected during ----
17:43 dbolser ----       LDS/Bio-SamTools-1.21.tar.gz       ---- Module::Build [build_requires]
17:44 dbolser I have installed Module::Build six or seven times...
17:44 deafferret Module Build requires 23 installations    ;)
17:44 dbolser ahhh
17:44 deafferret perldoc Module::Build finds it?
17:45 dbolser yup, but cpan always installs it when I ask
17:45 dbolser perl -e 'use Bio::DB::Sam'
17:45 dbolser Can't locate Bio/DB/Sam.pm
17:45 deafferret gist the whole install attempt output?
17:46 dbolser ok
17:46 dbolser gist = paste in chan?
17:46 dbolser ;-)
17:47 deafferret gist.   .... why you!! one of these days, Alice!
17:47 dbolser nyuk nyuk byuk
17:47 dbolser hmm... its installing Module::Build... intersting!
17:47 dbolser D/DA/DAGOLDEN/Module-Build-0.3607.tar.gz is just needed temporarily during building or testing. Do you want to install it permanently? [yes] yes
17:48 dbolser perhasp I should tyeps 'for the love of god yes!!!!'
17:48 dbolser http://gist.github.com/658585
17:49 dbolser looks good right?
17:49 deafferret cpan    o conf build_requires_install_policy yes
17:49 deafferret prerequisites_policy follow
17:49 dbolser build_requires_install_policy undef
17:49 deafferret set it to 'yes'   :)
17:49 dbolser oh... 'yes' you say?
17:50 deafferret YES
17:50 dbolser build_requires_install_policy [yes]
17:50 * deafferret warms up his silliness smiter
17:51 dbolser http://gist.github.com/658585
17:52 deafferret Not installing because is only 'build_requires'
17:52 deafferret that was the "oops"
17:52 deafferret but now that you set that to 'yes' if you do it again you should be ok
17:52 dbolser wha?
17:52 deafferret or just install it manually
17:52 dbolser 23 times?
17:52 deafferret manually is only 6 times
17:52 dbolser look Module::Build
17:53 dbolser ./Build install
17:53 dbolser Building Module-Build
17:53 dbolser ...
17:53 dbolser I'd say it was installed
17:53 deafferret with    build_requires_install_policy [yes]     what you pasted shouldn't happen
17:53 dbolser ok...
17:54 deafferret or try YESDAMMIT   ;)
17:54 dbolser I will try again... from scratch .... again...
17:55 dbolser hmm... its installing Module::Build... intersting!
17:55 deafferret hmm?    just    cpan Bio::DB::Sam     and you should be good
17:55 dbolser orly?
17:55 dbolser I wonder why I didn't think of that ...
17:56 rbuels dbolser: you'd better not be using sudo for any of this.  if you are, *pow*, straight to the moon!
17:56 * dbolser kicks rbuels hard in teh pants
17:56 dbolser http://gist.github.com/658602
17:56 rbuels dbolser: oh you're such a good boy
17:57 dbolser ;-)
17:57 dbolser but but...
17:57 dbolser it still fails
17:57 rbuels oh, well, simple matter of programming
17:57 dbolser perl -e 'use Bio::DB::Sam'
17:57 * rbuels waves vaguely
17:57 dbolser Can't locate Bio/DB/Sam.pm
17:58 dbolser ing?
17:58 dbolser wtf?
17:58 dbolser /local/Scratch/dbolser/perl5/lib/perl5/​i386-linux-thread-multi/Bio/DB/Sam.pm#
17:58 dbolser why did it put it there?
17:58 dbolser /local/Scratch/dbolser???
17:58 dbolser where did it get that from?
17:59 dbolser PERL5LIB=/homes/dbolser/perl5/lib/perl5:/homes/​dbolser/perl5/lib/perl5/i386-linux-thread-multi
18:00 * dbolser has no clude
18:04 rbuels dbolser: i386-linux-thread-multi is your arch name
18:04 rbuels dbolser: Bio::DB::Sam probably has some XS bindings
18:04 rbuels dbolser: which are arch-specific
18:05 dbolser what does that mean?
18:05 rbuels dbolser: arch = architecture
18:05 dbolser yes I know that
18:05 deafferret except in St. Louis, MO
18:05 dbolser but why is it putting things under /local/Scratch?
18:05 rbuels dbolser: hell if i know
18:05 dbolser I ...
18:06 rbuels dbolser: you probably have a bit of Olde Configuration that is specifying that
18:06 * dbolser thinks about rm -rf ~/perl
18:06 dbolser right
18:06 rbuels dbolser: one of the best things ever is to keep your ~/perl in git
18:06 dbolser but where... how... why???
18:06 rbuels cd ~/perl;  git init;
18:06 dbolser ahhh
18:06 deafferret does perl -V have /local/Scratch in it anywhere?
18:06 dbolser I seem to remember this exact convo
18:07 dbolser perl -V | grep -i scratch | wc -l # = 0
18:07 deafferret "Binary file matches"       (grep jokes rule!)
18:08 dbolser deafferret: you're right
18:08 dbolser prolly
18:09 dbolser rbuels: can you help me confirm that my local::lib is correct before I trash my ~/perl and start again?
18:09 dbolser (I'll put it in git promptly after)
18:10 dbolser because.... if I trash ~/perl, I guess I'll loose local::lib too right?
18:10 rbuels dbolser: well, grep -R /local/Scratch ~/perl first
18:10 rbuels dbolser: you probably don't have to trash everything
18:10 deafferret fuck it. use Scala instead.
18:11 rbuels dbolser: env | grep /local/Scratch
18:11 rbuels dbolser: it's probably either going to be in 1.) your perl itself, 2.) your ~/perl, or 3.) your environment
18:11 rbuels those are the three usual places to look
18:12 dbolser env | grep /local/Scratch nothing
18:12 dbolser env | grep /local/Scratch # #nothing
18:12 dbolser right
18:12 dbolser env was the first place I looked, thanks to deafferret I looked in perl, which leaves ~/perl...
18:12 dbolser shedloads...
18:12 rbuels eh?
18:13 * rbuels paints the shed blue
18:13 dbolser grep -R /local/Scratch ~/perl5/ | wc -l # 4870
18:13 deafferret Note: <tfoot> must appear before <tbody> within a table, so that a browser can render the foot before receiving all the rows of data.
18:13 deafferret what... the... frack
18:14 rbuels deafferret: wtfrack?
18:14 deafferret http://www.w3schools.com/tags/tag_tbody.asp
18:15 dbolser is it trashing time?
18:16 dbolser e.g. /homes/dbolser/perl5/lib/perl5/i386-linu​x-thread-multi/auto/Bio/.packlist:/local​/Scratch/dbolser/perl5/bin/bp_aacomp.pl
18:16 rbuels dbolser: well, .packlists don't matter
18:17 rbuels dbolser: wait, did you *move* this local::lib?
18:17 rbuels dbolser: from /local/Scratch?
18:17 dbolser iirc no
18:17 rbuels dbolser: yes you did.
18:17 dbolser I *did* use /local/Scratch a long time ago
18:17 rbuels dbolser: if the .packlists have that in it.
18:17 * rbuels dances around like a schoolboy chanting 'you moved it'
18:18 * dbolser wimpers
18:18 rbuels lol
18:18 dbolser Binary file /homes/dbolser/perl5/lib/perl5/i386-linu​x-thread-multi/auto/HTML/Strip/Strip.so matches
18:18 dbolser ;-)
18:18 rbuels agh, you're boned
18:18 dbolser rm -rf ~/perl?
18:18 rbuels dbolser: you can't move local::lib dirs.
18:18 dbolser re-install local::lib?
18:18 rbuels unfortunately.
18:18 rbuels dbolser: well, for one, use cpanm.
18:18 dbolser cpanm?
18:19 rbuels dbolser: http://search.cpan.org/~miyagawa/App-​cpanminus-1.0015/lib/App/cpanminus.pm
18:19 dbolser # Are you on drugs?
18:19 rbuels dbolser: try this
18:19 * rbuels types
18:19 * dbolser readies his kbd
18:20 rbuels mv ~/perl ~/notperl;  wget -O - http://cpanmin.us | perl - -L ~/perl --self-upgrade local::lib
18:20 rbuels dbolser: and that should get you a new local::lib bootstrapped in ~/perl
18:20 rbuels echo installdeps --cpan_client $HOME/perl/bin/cpanm >> ~/perl/.modulebuildrc
18:21 dbolser assuming local::lib bootstraps cleanly in centos...
18:21 * rbuels cringes
18:21 dbolser which it has been known to fail under ;-)
18:21 dbolser something is happening
18:22 dbolser you are an advocate of changing more than one thing at once?
18:22 pyrimidine joined #bioperl
18:22 * dbolser blogs about how cool rbuels is
18:23 rbuels dbolser: changing lots of things at once is Progress!
18:24 dbolser http://bioblog5000.blogspot.com/2010/11/p​roblems-with-your-local-perl-install.html
18:25 dbolser file /usr/share/man/man3/DateTime:​:TimeZone::Local::VMS.3pm.gz conflicts between attempted installs of perl-DateTime-0.4501-3_1.el5.i386 and perl-DateTime-TimeZone-0.6904-1.el5.centos.noarch
18:25 dbolser (but that was my yum based lunacy, not your command)
18:25 rbuels o_O
18:26 deafferret eww... packages for CPAN is fail
18:26 deafferret they can never keep up with the awesome that is CPAN
18:26 * rbuels wonders why dbolser is using legacy rpm stuff
18:26 deafferret (fsvo awesome)
18:26 rbuels lol
18:26 pyrimidine huh, didn't see that Lincoln released an update to Bio-Samtools
18:26 dbolser fsvo?
18:26 deafferret for some values of
18:27 * deafferret shakes javascript violently
18:27 dbolser rbuels: well... that command has finished
18:27 dbolser and ... no errors sofa
18:28 dbolser ls ~/perl5/lib/perl5/# about 26 things
18:28 dbolser (its ~perl5, not ~perl like I wrote, but I changed your command)
18:29 pyrimidine huh, didn't see that Lincoln released an update to Bio-Samtools that doesn't compile
18:29 dbolser so my .bash_profile has "eval $(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)
18:29 dbolser "
18:29 dbolser pyrimidine: trash your ~perl5 ...
18:29 pyrimidine sorry, that should be "doesn't pass tests"
18:30 pyrimidine it's missing a file: t/data/dm3_3R_4766911_4767130.sam.sorted.bam
18:30 pyrimidine compiles fine
18:30 dbolser rbuels: some fancy perl command to test what we just did?
18:31 rbuels dbolser: perl -Mlocal::lib ?
18:31 rbuels dbolser: perl -Mlocal::lib  -e 42
18:31 rbuels something like that
18:32 dbolser seems good
18:32 dbolser http://gist.github.com/658653
18:33 dbolser now to install bioperl...
18:33 dbolser GAH!
18:33 rbuels dbolser: git init
18:34 rbuels dbolser: store your ~/perl5 in git
18:34 rbuels dbolser: it's so fun
18:34 dbolser oh right
18:34 dbolser Initialized empty Git repository in .git/
18:35 rbuels dbolser: git add . ; git commit -m 'initial import'
18:35 dbolser oh right
18:36 dbolser cpanm Bio::DB::Sam ?
18:38 rbuels dbolser: yep
18:38 rbuels dbolser: and then you can use git to see *exactly* what it did
18:38 rbuels dbolser: and commit if it worked ok
18:38 rbuels dbolser: once your local::lib is in git, you can do lots of stuff
18:39 dbolser ic
18:39 rbuels dbolser: like if something is breaking, just edit it in there
18:39 rbuels dbolser: to insert debugging or whatever
18:39 rbuels dbolser: and then just reset --hard to get rid of it
18:39 rbuels dbolser: after you figure out what is going on
18:39 rbuels etc etc
18:40 dbolser rbuels: how would you like me to acknowledge you on that blog post?
18:40 dbolser (just adding deets)
18:40 dbolser Found dependencies: Bio::Root::Version # ;-)
18:41 dbolser Building and testing BioPerl-1.006001
18:41 rbuels dbolser: what blog post?
18:41 dbolser http://bioblog5000.blogspot.com/2010/11/p​roblems-with-your-local-perl-install.html
18:42 rbuels dbolser: lol
18:42 dbolser I'm the blogbot
18:43 dbolser Building and testing Bio-SamTools-1.21 ... OK
18:43 dbolser Successfully installed Bio-SamTools-1.21
18:43 rbuels dbolser: the command didn't quite come through correctly
18:43 dbolser oh
18:43 rbuels dbolser: just acknowledge me as rbuels i guess
18:43 rbuels dbolser: and link to my gmod user page i gues
18:43 rbuels s
18:44 dbolser linky?
18:44 rbuels dbolser: http://gmod.org/wiki/User:RobertBuels
18:44 dbolser ty
18:45 dbolser I was asked to start this blog on #perl because there is some kind of perl blog coalition
18:45 dbolser because nobody blogs about perl!
18:45 dbolser did you watch that ruby vid I posted?
18:46 dbolser (on #gmod)
18:46 dbolser thanks so much for this help rob
18:47 * dbolser goes home
18:47 pyrimidine rbuels is such a great li'l helper
18:47 rbuels dbolser: no problem
18:47 rbuels thank miyagawa.
18:48 pyrimidine cpanm is nice
18:48 dbolser miyagawa?
18:48 dbolser ohic
18:48 dbolser http://bioblog5000.blogspot.com/2010/11/p​roblems-with-your-local-perl-install.html ## <- current final version, any suggestions for changes welcome
18:48 pyrimidine rbuels: never thought about using git for that, but it makes perfect sense
18:49 rbuels dbolser: ~/perl, not -/perl
18:49 rbuels several other instances of that in there
18:49 rbuels dbolser: also, there is inconsistency between ~/perl and ~/perl5
18:50 rbuels dbolser: pick one or the other
18:50 dbolser I should "git add . ; git commit -m 'bioperl and Bio::DB::Sam installed'" once I confirm it's working?
18:50 pyrimidine Bio-Samtools v 1.23 is on its way, perl LS
18:50 rbuels dbolser: yeah that too
18:50 dbolser ty
18:50 pyrimidine s/perl/per/
18:51 dbolser -perl must be an optical illusion
18:56 dbolser night
19:00 rbuels night
19:03 deafferret no it's not
19:10 pyrimidine yes it is
19:10 deafferret but but but
19:10 * pyrimidine is feeling contrarian today
19:10 pyrimidine :)
19:11 pyrimidine no but's
19:11 * pyrimidine is working on his parenting skills
19:16 deafferret ha!!! javascript you bastard
19:21 deafferret (Joan Osborne)++ # Right Hand Man
20:23 pyrimidine Dist::Zilla for the win!
20:50 bag__ joined #bioperl
20:57 rbuels pyrimidine: if i keep writing emails like that people are going to get pissed off i bet
20:57 * rbuels puts on his asbestos underwear
20:58 pyrimidine rbuels: well, maybe, but what would be their argument?
20:59 pyrimidine I kind of understand maybe Lincoln not having the time to learn something like Dist::Zilla, but he is using git
20:59 rbuels who needs an argument when you are just plain tired of the little twerp telling you how behind the times you are, lol
21:00 pyrimidine I think all groups need someone to stir the pot, as long as it's done in a positive way
21:00 pyrimidine less "you're code is shit", more "hmm, this is a better way to do things"
21:02 pyrimidine rbuels: and, if we waited for someone else to do something (like move bioperl to git, make changes to gff validation, etc) we would probably wait forever
21:02 * rbuels nods
21:02 rbuels oh, you don't see me *not* doing these things
21:02 rbuels o_O
21:02 pyrimidine (of course, we're waiting for that next bioperl release still..... :)
21:02 rbuels yeah .....
21:03 rbuels i haven't gotten much traction on that have it
21:03 rbuels er, I
21:06 pyrimidine we all have daily $jobs that take time; there are only a few things that need to be checked in prior to an alpha
21:06 rbuels well, what about the Big Split though
21:06 rbuels that's what i was saying i haven't gotten traction on
21:06 pyrimidine ah
21:07 rbuels mostly because it's hard, lol
21:07 pyrimidine we can probably work some on that next week
21:07 rbuels aiiieee it's next week
21:07 pyrimidine :)
21:11 pyrimidine we'll have a number of bioperl devs present, as well as dukeleto, correct?
21:11 pyrimidine possibly Lincoln (though I last heard maybe not)
21:15 rbuels pyrimidine: looks like lincoln will not be there
21:15 rbuels pyrimidine: dukeleto will be.
21:15 pyrimidine okay
21:16 pyrimidine rbuels: so, we may have enough to brainstorm some
21:16 * rbuels nods
21:16 pyrimidine over beers, of course :)
21:18 rbuels pyrimidine: we should brainstorm about the genomes-as-connected-graphs-of-similarity model
21:19 rbuels pyrimidine: it's actually a little bit similar to git's data model of connected graphs of commits.
21:19 rbuels but in more dimensions
21:33 rbuels pyrimidine, dukeleto: literature search about that: http://www.springerlink.com​/content/d34102n4132236h7/  http://bioinformatics.oxfordjournals.​org/content/18/suppl_1/S303.abstract
21:35 rbuels the key to the whole thing is finding a performant way of storing and working with that kind of data for arbitrary numbers of genomes
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22:41 * deafferret shorts rbuels' stock

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