Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-05-12

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All times shown according to UTC.

Time Nick Message
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15:07 jhannah @@@@   @
15:11 rbuels whoa.
15:12 rbuels did you go try for that huge-pizza-and-get-some-award thing last night?
15:13 jhannah phant ate the leftovers from odlug
15:35 vinnana joined #bioperl
15:37 vinnana hi all. If i read in the following bed-file line into bioperl using Bio::FeatureIO
15:37 vinnana chr101match.chr1.101-200.+.1
15:37 vinnana i get a feature with start 0 and end 0 (bioperl 1.6.1).
15:38 rbuels hrmm...
15:38 * rbuels knows nothing about bed files
15:38 rbuels jhannah?
15:38 vinnana That's against the specification.
15:38 vinnana http://genome.ucsc.edu/FAQ/FAQformat.html#format1
15:39 jhannah .bed files?
15:39 vinnana it should be start 1, end 1 in bioperl positions (1-based, last base inclusive)
15:39 vinnana Yes.
15:40 jhannah vinnana: i would love you forever if you patched on github
15:40 jhannah if you're not ready for that I can try to field the concern, or you can file a bugzilla
15:40 jhannah is there any t/ of .bed files?
15:40 vinnana t/ ?
15:40 jhannah vinnana: I have no idea your level of Perl-fu
15:40 jhannah :)
15:41 rbuels t/ is the usual dir for perl tests
15:41 vinnana jhannah: 10 years or so
15:41 rbuels inside a distribution.
15:41 jhannah vinnana: ooo... welcome to bioperl committers then!  ;)
15:41 vinnana oh that's what you mean
15:41 vinnana ill check for the tests
15:42 jhannah vinnana++
15:42 jhannah abooz: what's the status of the .gff glitch?
15:43 jhannah vinnana: we just moved to github... this morning. so you'll want to clone that... or fork it, or whatever makes you happy
15:44 jhannah http://github.com/bioperl/bioperl-live
15:45 vinnana jhanna: fine I'll do that; can't find any test for .bed in FeatureIO.t
15:46 * jhannah looks
15:46 vinnana thanks, CU
15:46 jhannah leaving so soon?  :(
15:47 jhannah Hudson seems freaking neato
15:47 * jhannah digs the SVN integration
15:47 vinnana left #bioperl
15:47 * jhannah sighs
15:48 rbuels hudson?
15:49 jhannah http://hudson-ci.org/
15:49 jhannah those damn java guys flauted their superior CI wheel at me last night
15:50 * jhannah shakes his fist at his coffee
15:50 jhannah svn: Can't connect to host 'code.open-bio.org': Connection timed out
15:50 jhannah "read-only" has been redefined  :)
15:51 rbuels the read-only mirror is on a different server
15:51 rbuels jhannah: ^^^
15:52 jhannah dev.open-bio.org is still up
16:11 abooz jhannah: sorted it on my local repo
16:11 jhannah so you have a fixed git commit?
16:11 abooz yes.
16:12 jhannah woot! is it somewhere I can pull it?
16:12 abooz hmm..my local repo ..
16:13 abooz not exported online.
16:13 abooz i can give you a diff if you want.
16:14 driveby_bot joined #bioperl
16:14 driveby_bot /home/svn-repositories/bioperl: r16984 (sharpton) : Amended alignment extraction code in hmmer3 SearchIO parser to correctly extract query and hit strings from a hsp.
16:14 driveby_bot Diff: http://tinyurl.com/2abva6a
16:14 jhannah whoah... umm... so SVN is still alive apparently   :)
16:16 jhannah abooz: do you have a github account?
16:19 abooz nope.
16:19 abooz i'll create one.
16:25 Jun What does github do?
16:25 perl_splut same thing as SVN or CVS
16:26 Jun ok... no idea what they are either...
16:26 jhannah version control systems  :)
16:26 jhannah so you know who changed what source code when
16:26 jhannah github.com
16:27 abooz ok i've created a github account. The changes i made were on a git clone of bioperl-live
16:28 Jun ok, now i see
16:28 abooz how do i push
16:28 jhannah um   :)
16:28 rbuels Jun: have you been in contact with Chris, getting ready to code?
16:28 Jun I just created a github account. So the free account is enough, right?
16:28 rbuels Jun: yes, free is enough
16:28 Jun yep, check my blog
16:28 jhannah abooz: usually you would have clicked the clone button inside github, then pulled, then patched, then pushed
16:28 rbuels Jun: link?
16:29 Jun http://gsoc2010-junyin.blogspot.com/
16:29 Jun not too many things. but I've found a few things to do now...
16:29 jhannah abooz: I'm NOT good at git yet. slowly getting better
16:31 abooz right. Pull means merging i think, so if i pull it now it will merge.but which repo do i do the changes on?
16:31 abooz it needs to be tested before i guess.
16:31 rbuels abooz, Jun: you guys need to read some of the git intro documentation when you get a change
16:31 rbuels er, chance
16:32 rbuels a lot of it is linked from git-scm.com
16:32 Jun yep, just got signed up in git
16:33 Jun Chris also told me to work on the git, though I dont have any clue how to use it yet.
16:33 Jun I will look into it~
16:38 Jun It seems the comment links in the git are not very good. When you click them, it says no such page...
16:39 Jun but when you look for it in the "commits", you can actually find them.
16:43 rbuels Jun: the tool is called just "git".  there are a number of websites that integrate with it, one of them is github.com
16:44 rbuels http://git-scm.com/documentation
16:45 Jun I see, very interesting... :D
16:51 abooz so to create a brach, i create a branch and github will see it (and create it remotely) once i push it, right?
16:55 jhannah abooz: after the push, yes
16:55 jhannah the branches all sync on push/pull is my understanding
16:55 jhannah (branches are just alias names on specific commits, which all flow during push/pull)
16:56 jhannah (and/or I have no idea what I'm talking about)
17:51 rbuels Jun: could you add a link to your blog to http://open-bio.org/wiki/Google_Summer_of_Code
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19:05 pyrimidine seems there is a delay with github service hooks getting set up properly
19:09 pyrimidine okay, two popped up on bioperl-guts (one several days old), maybe a white-list thingy, but they aren't working on IRC yet
19:09 rbuels pyrimidine: what service hooks are you using
19:09 rbuels pyrimidine: commit emails?
19:10 pyrimidine yes
19:10 pyrimidine would be nice to set up a URL for webhooks
19:11 rbuels pyrimidine: i have a cgi that can take github POSTs
19:11 pyrimidine ooh, that would be nice
19:11 rbuels pyrimidine: right now it makes commit emails (in a nicer format)
19:11 * rbuels nopastes it
19:11 pyrimidine okay
19:12 rbuels http://gist.github.com/399015
19:12 rbuels pyrimidine: ^^^
19:13 pyrimidine got it
19:14 deafferret y'all++
19:15 rbuels pyrimidine: i forwarded you an example of the commit emails it makes
19:16 pyrimidine of course, this is the time my email craps out
19:17 pyrimidine :-/
19:20 pyrimidine okay, got it.  That would work, wondering if the best place for it would be on an open-bio server
19:21 rbuels pyrimidine: yes, if your problem is the crazy filtering they do
19:23 rbuels hrm, actually now that i look at it again it does not use Tie::Function
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19:34 rbuels pyrimidine: do you remember if we have talked about requiring gsoc students to have a blog?
19:35 pyrimidine no, but I already mentioned this to Jun
19:35 rbuels pyrimidine: seems like we would have had this discussion among gsoc mentors, but i don't recall having it
19:35 pyrimidine okay
19:35 pyrimidine we can bring this up on the soc maillist.
19:35 rbuels ok, i'm about to send a poking "make sure your students are getting their bearings" email to gsoc-mentors
19:35 rbuels i'll put it in there
19:37 rbuels ok, sent
19:40 pyrimidine ok
19:41 pyrimidine wish github would fix that 'copy permissions' thing.  talk about bad timing.
19:53 github joined #bioperl
19:53 github bioperl-live: master DaveMessina * 3e1518a (1 files in 1 dirs): s/Subversion/Git/ and testing git - http://bit.ly/cCWc6r
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19:58 pyrimidine could prob add an IRC hook in to that script as well
19:58 rbuels pyrimidine: lots of things could be done to that script ....
19:59 rbuels erm, does the github irc bot make one line per commit?
20:04 pyrimidine yes
20:04 pyrimidine it could be made to git more
20:04 pyrimidine *give
20:04 * pyrimidine typing 'git' too much today
20:06 perl_splut heheh
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21:47 deafferret git r done!
21:48 deafferret Larry the Cable guy is from Omaha. He's a physique example for all of us.
21:54 perl_splut physique example?
21:56 deafferret he's very athletic
21:57 deafferret like me
22:18 spekki01 Since i don't have root access i created a local directory to install bioperl and some other perl modules to, its in ~/perl5. Now in my perl script i put the line use lib "~/perl5/" right before use Bio::Perl; followed by use LWP::Simple; and use XML::Twig; and for some reason i always get the error that i dont have twig isntalled. Am i doing the syntax wrong for loading the local modules?
22:19 perl_splut do you have twig installed?
22:20 deafferret spekki01: most of bioperl works fine without installing it. but that's not generally true of CPAN
22:20 deafferret spekki01: so you might need to build your own perl so you can do whatever you want, or use local::lib to install XML::Twig to a specific location in your home directory
22:22 spekki01 its hard to say, because i went to the cpan website downloaded XML-Twig-3.34.tar.gz installed it and after looking where it installed it put a couple thing in my perl5/bin directory "xml_grep, xml_merge, xml_pp, etc..." but nothing that is specifically twig i want to say.
22:23 spekki01 yeah i was trying to figure out local::lib but i could not get it working for some reason
22:24 perl_splut so, in one of your library folders do you have XML/Twig? as a folder and child folder?
22:24 deafferret perldoc -l XML::Twig
22:25 deafferret local::lib is very slick, and can save you in some circumstances.  irc.perl.org #local-lib
22:26 spekki01 yeah in my ~/perl5/XML/Twig
22:26 spekki01 but the Twig directory is empty
22:27 perl_splut is there an XML::Twig.pm?
22:27 perl_splut sorry
22:27 perl_splut XML/Twig.pm
22:27 spekki01 deafferret: ill check that channel in a bit thanks
22:27 spekki01 no nothing in it, lemme do a quick search for Twig.pm in that whole perl5 directory
22:28 perl_splut I didn't say in it, heheh
22:28 perl_splut ~/perl5/XML/Twig.pm <---
22:29 perl_splut and what method did you use to "install" the package?
22:29 deafferret you should also have an XML/Twig/Xpath.pm
22:30 spekki01 k in the ~/perl5/XML/ directory there is not Twig.pm but when i did a search it shows up in 2 spots withing the bioperl install, ill tell you the install method in a sec
22:30 deafferret no perl_splut  :(  http://bioperl.org/wiki/IRC
22:31 deafferret updatedb       ?
22:31 perl_splut and never shall it exist, deafferret
22:31 deafferret boo!
22:33 deafferret uhoh... what did I do?
22:33 spekki01 perl Makefile.PL PREFIX=~/perl5       followed by make, make test, make install, make clean
22:33 spekki01 the makefile is in the xml-twig directory after unpacking it
22:34 perl_splut p and s are redundant
22:34 deafferret um, is ~/perl5  in your perl -V  ?
22:34 spekki01 checking..
22:34 spekki01 yes its the second entry
22:35 spekki01 oh wait
22:35 spekki01 maybe not
22:35 perl_splut so, this isn't a registered channel with chanserv anymore?
22:36 deafferret I know nothing about Freenode juju
22:36 perl_splut p == private, s == secret, r == registered channel
22:36 perl_splut it isn't freenode juju... it is irc juju set by the various bots
22:37 spekki01 no actually a sub directory farther down in the ~/perl5 directory is listed in the @INC
22:37 perl_splut and if you're going to add or remove flags, you might want to look up what they are and do before doing so, heheh
22:37 spekki01 what is the command to modify the @INC variable in a bash shell?
22:38 deafferret perl_splut: ya, I did +h on YOU which on irc.perl.org gives you half-ops, but here does... +prs
22:38 perl_splut strange bot juju
22:38 perl_splut http://www.perlhowto.com/e​xtending_the_library_path
22:39 spekki01 but from reading doesn modifying the use lib in the perl script change where the @INC will look?
22:39 spekki01 doesnt*
22:40 perl_splut Perl will look for modules in the directories specified in PERL5LIB environment variable before looking in the standard library and current directory, so you can set this variable to locate your modules.
22:41 deafferret spekki01: yes, if you want to 'use Baz;' from Foo/Bar/Baz.pm then you could 'use lib Foo/Bar; use Baz;'
22:41 deafferret and/or PERL5LIB and/or perl -I
22:43 perl_splut PERL5LIB is how you do it for BASH shell
22:43 perl_splut PERL5LIB=/home/path/lib:/usr/another/path/lib; export PERL5LIB
22:52 spekki01 still nothing even after setting that PER5LIB variable i get http://codepad.org/rLiC7PwZ
22:54 spekki01 oh well im done for the day I'll attempt to figure it out tomorrow, thanks for the help guys :)
23:00 deafferret spekki01: ping
23:00 deafferret spekki01: I think that's a BioPerl ./Build.PL thing
23:01 deafferret ./Build.PL asks you questions and then modifies files to block stuff like that based on the (quite possibly outdated) belief that you didn't have XML::Twig installed at the time
23:01 deafferret I don't really understand why BioPerl does this
23:02 deafferret & jQuery mtg

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