Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-07-08

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All times shown according to UTC.

Time Nick Message
00:00 deafferret PERL5LIB is built into perl
00:00 Emos ah ok
00:07 Emos I think I finally got it installed
00:07 deafferret I give up.   Send http://github.com/jhannah/sandb​ox/blob/master/emos/ensembl.pl to ensembl-dev, see if they can tell you
00:07 Emos why are you giving up?
00:08 Emos didn't you already accomplish the task?
00:08 Emos I thought you found a way of annotating
00:08 deafferret cause I've blindly tried 25 things, none of them work, and this isn't a bioperl problem  :)
00:08 deafferret nope. I can't fetch NT_025741.15 which is what you need
00:08 Emos I mean
00:08 Emos it's ok $slice = $slice_adaptor->fetch_by_region( 'chromosome', '20', 100000, 101000 );
00:09 deafferret yup. that works. but you don't want chr20, you want NT_025741.15   :)
00:09 Emos ok, but then if I can insert instead of 'chromosome', '20', 100000, 101000
00:10 Emos the variables from the script my $db = new Bio::DB::EntrezGene;
00:10 Emos that you managed this morning
00:10 Emos I'm ok
00:10 deafferret right. and the first example is NT_025741.15, which you cannot map to anything
00:11 Emos I mean I need a general way to look up
00:11 Emos from an ensembl code
00:11 Emos the sequence of the gene and its flankng regions
00:12 deafferret yup. entrezID 54806 -> NT_025741.15 -> FAIL
00:12 Emos BUT, if we don't care about the contig a I don't care, we can work only on sequence
00:13 Emos entrez ID-> position -> add 100kb at each side->get the sequence
00:13 deafferret do you know which chr you're on?
00:13 Emos we must ask the first script
00:13 Emos http://pastebin.com/d51544b65
00:19 Emos http://doc.bioperl.org/releases/b​ioperl-1.6.0/Bio/DB/BioFetch.html
00:24 deafferret this works:  http://github.com/jhannah/sa​ndbox/blob/master/emos/x.pl
00:24 deafferret you have a bunch of Entrez IDs?
00:25 Emos yes
00:25 deafferret give me the next 2
00:26 Emos damn
00:26 Emos Can't locate DBD/mysql.pm in @INC
00:26 Emos wait a moment
00:27 Emos I give you what you ask
00:28 Emos 27185, 1815, 280730
00:28 Emos for example
00:29 Emos 581
00:30 Emos what is DBD?
00:30 deafferret database driver
00:30 Emos how to install it? with fink?
00:31 deafferret cpan DBD::mysql
00:33 deafferret boo-ya. this is 100% what you wanted... i think...  http://github.com/jhannah/sa​ndbox/blob/master/emos/x.pl
00:33 deafferret jhannah@klab:~/src/sandbox/emos$ perl x.pl
00:33 deafferret 54806 chr6 39674566..40088359
00:33 deafferret 27185 chr1 25180339..25794796
00:33 deafferret 1815 chr11 477304..680702
00:33 deafferret 280730 chr18 316898..520907
00:33 deafferret 581 chr19 21626334..21833272
00:34 Emos WONDERFUL!!
00:35 Emos but I cannot make it work here
00:35 Emos wait a minute
00:35 Emos Can't locate Bio/EnsEMBL/Registry.pm in @INC
00:36 deafferret add that use lib line I mentioned above
00:36 deafferret or perl -I
00:36 Emos echo $PERL5LIB
00:36 Emos /sw/lib/perl5:/sw/lib/perl5/darwin
00:37 Emos I had added all the things to PERL5LIB before
00:37 Emos but now they are gone
00:37 Emos did I have to save them?
00:37 deafferret use lib "/Users/yourusername/src/ensembl/modules";   in your prog
00:38 Emos this doesn't work
00:38 Emos use" not allowed in expression at prova line 8, at end of line
00:39 deafferret you must have a typo
00:40 Emos now
00:40 Emos echo $PERL5LIB
00:40 Emos /sw/lib/perl5:/sw/lib/perl5/darwin:$/User​s/EmanueleO/src/bioperl-live:$/Users/Eman​ueleO/src/ensembl/modules:$/Users/Emanuel​eO/src/ensembl-compara/modules:$/Users/Em​anueleO/src/ensembl-variation/modules
00:41 deafferret those $ are bad
00:41 deafferret add    use lib "/Users/EmanueleO/src/ensembl-compara/modules";    # to your prog
00:43 Emos echo $PERL5LIB
00:43 Emos /sw/lib/perl5:/sw/lib/perl5/darwin:$/Users/Ema​nueleO/src/bioperl-live:$/Users/EmanueleO/src/​ensembl/modules:$/Users/EmanueleO/src/ensembl-​compara/modules:$/Users/EmanueleO/src/ensembl-​variation/modules:/Users/EmanueleO/src/bioperl​-live:/Users/EmanueleO/src/ensembl/modules:/Us​ers/EmanueleO/src/ensembl-compara/modules:/Use​rs/EmanueleO/src/ensembl-variation/modules
00:43 deafferret ls -al /Users/EmanueleO/src/ensembl-compa​ra/modules/Bio/EnsEMBL/Registry.pm
00:44 Emos no such file or drectory
00:45 deafferret add    use lib "/Users/EmanueleO/src/ensembl/modules";    # to your prog
00:45 deafferret (no -compara)
00:45 deafferret assuming that's where you put Bio/EnsEMBL/Registry.pm
00:46 deafferret I only downloaded ensembl. I didn't do the other 4
00:46 Emos Can't locate object method "load_registry_from_db" via package "Bio::EnsEMBL::Registry" (perhaps you forgot to load "Bio::EnsEMBL::Registry"?) at prova line 14.
00:47 deafferret do you have the     use Bio::EnsEMBL::Registry;   line at the top like I do?
00:47 Emos because I commented use Bio::Ensembl::Registry
00:47 * deafferret pokes Emos
00:47 Emos but if I uncomment it
00:48 Emos Compilation failed in require at prova line 8.
00:48 Emos BEGIN failed--compilation aborted at prova line 8.
00:48 deafferret that makes no sense. nopaste your code
00:48 deafferret http://pastebin.com/
00:48 deafferret copy/paste error?   http://github.com/jhannah/sa​ndbox/blob/master/emos/x.pl
00:50 Emos Can't locate DBD/mysql.pm in @INC
00:50 deafferret where the *bleep* are you trying to use mysql?
00:51 Emos wait a momento
00:53 Emos http://pastebin.com/d1ed79fde
00:54 deafferret show me your code
00:54 Emos http://pastebin.com/d4dec7700
00:54 Emos I cannot install DBD
00:54 Emos the code is copied and pasted directly from  http://github.com/jhannah/sa​ndbox/blob/master/emos/x.pl
00:54 deafferret do you have MySQL installed on your computer?
00:55 deafferret x.pl should have nothing to do with MySQL
00:56 deafferret when you run x.pl it bitches about DBD::mysql?
00:57 Emos maybe I just pasted the wrong code of the sandbox
00:58 Emos no
00:58 Emos it asks me DBD
00:58 Emos I don't know why
00:59 deafferret well, Bio::EnsEMBL::Registry is truly evil if it's requiring MySQL for no reason.
01:00 deafferret perl -MCPAN -e shell     force install DBD::mysql
01:02 Emos Failed during this command:
01:02 Emos CAPTTOFU/DBD-mysql-4.012.tar.gz              : writemakefile NO '/usr/bin/perl Makefile.PL' returned status 512
01:02 deafferret wget http://search.cpan.org/CPAN/authors/id​/C/CA/CAPTTOFU/DBD-mysql-4.012.tar.gz
01:03 deafferret tar xvzf DBD-mysql-4.012.tar.gz
01:03 deafferret cd DBD-mysql-4.012
01:03 deafferret perl Makefile.PL
01:03 deafferret make
01:03 deafferret make install
01:03 deafferret (might not work)
01:03 * deafferret shakes his fist at Bio::EnsEMBL::Registry
01:04 Emos in which folder do i have to do that?
01:04 deafferret src
01:04 Emos can I use fink?
01:04 deafferret dunno
01:04 deafferret DBD::mysql won't REALLY install unless you install MySQL itself
01:04 deafferret so if you want to install MySQL, feel free
01:04 deafferret then DBD::mysql might actually work
01:05 deafferret but you don't need it to WORK, you just need Bio::EnsEMBL::Registry to think it is
01:05 * deafferret shakes his fist at Bio::EnsEMBL::Registry
01:06 deafferret crap. next $work project is yuck
01:06 Emos :-(
01:07 Emos about what?
01:07 deafferret https://ssl.omnihotels.com   cookie problem  :(  bah
01:08 Emos :-(:-(
01:08 deafferret $day; $dollar++;
01:08 deafferret $day++; $dollar++;
01:08 deafferret $older++; $debt++;   :)
01:09 * deafferret owes his soul to the company store
01:09 * deafferret loads 16 tons
01:45 Emos I installed mysql qith fink
01:46 Emos but DBD won't install
01:46 Emos :-(
01:46 Emos very sad
01:46 Emos can't use your perfect script
01:46 Emos Cannot find the file 'mysql_config'
01:46 Emos that's the problem
01:47 deafferret did you try DBD-mysql-4.012.tar.gz ?
01:47 Emos yeah
01:47 Emos the same
01:47 Emos when i say make.pl
01:47 Emos it gets stuck
01:47 Emos Cannot find the file 'mysql_config'
01:48 deafferret you meant 'make' right?
01:48 Emos can't exec "mysql_config": No such file or directory at Makefile.PL line 82.
01:48 Emos annot find the file 'mysql_config'! Your execution PATH doesn't seem
01:48 Emos not contain the path to mysql_config. Resorting to guessed values!
01:48 Emos Can't exec "mysql_config": No such file or directory at Makefile.PL line 464.
01:48 Emos Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located
01:49 Emos Can't exec "mysql_config": No such file or directory at Makefile.PL line 464.
01:49 Emos Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located
01:49 Emos Can't exec "mysql_config": No such file or directory at Makefile.PL line 464.
01:49 Emos Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located
01:50 deafferret so when you searchlight (or whatever that thing in the upper right corner is called) for mysql_config there's no hits?
01:50 deafferret http://www.nntp.perl.org/group/p​erl.macosx/2007/09/msg10387.html
01:51 Emos no
01:54 deafferret does this install mysql_config?  http://dev.mysql.com/downloa​ds/mysql/5.1.html#macosx-dmg
02:00 Emos http://search.cpan.org/dist/DBD-​mysql/lib/DBD/mysql/INSTALL.pod
02:01 Emos there's a way of installing it without mysql_config
02:01 Emos but i don't understand how
02:06 deafferret dunno. DBD::mysql installs fine on Linux. I've never tried on OS X
02:06 deafferret no Mac here
02:09 Emos is there a command
02:09 Emos to search for a file
02:09 Emos with commandline?
02:09 deafferret find
02:10 Emos i typed find mysql_config
02:10 Emos it tells me no such file or directory
02:10 Emos without searching
02:10 deafferret find / -name "mysql_config"
02:11 deafferret that's the same this searchlight does, only searchlight is faster (indexed)
02:12 Emos but i think spotlight skips system files
02:14 deafferret oh? perhaps
02:15 Emos found
02:15 Emos how can i feed it to the isntaller script?
02:15 deafferret put it in your $PATH
02:15 Emos ??
02:15 deafferret same problem as $PERL5LIB
02:15 deafferret echo $PATH
02:16 Emos it doesnt paste here
02:16 Emos but is "/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbi​n:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin"
02:16 Emos ok
02:17 Emos how can i put it in $path?
02:19 deafferret if you can't figure out how to change your environment variables, then copy the program into one of those directories
02:20 Emos wait
02:20 Emos maybe i did it
02:20 Emos WE did it
02:21 Emos macos:perl EmanueleO$ perl prova3
02:21 Emos 54806 chr6 39674566..40088359
02:21 Emos 27185 chr1 25180339..25794796
02:21 Emos 1815 chr11 477304..680702
02:21 Emos 280730 chr18 316898..520907
02:21 deafferret woot!
02:21 Emos 581 chr19 21626334..21833272
02:21 Emos macos:perl EmanueleO$
02:21 Emos YUHOOOOO
02:22 deafferret out.fasta should be sitting there
02:25 Emos YES!!!!
05:20 rbuels deafferret: you have saint-like patience.
05:21 deafferret rbuels: I agree. I am awesome.
05:22 rbuels i could not do what you did with Emos.
05:22 rbuels start to end, that was 9 hours.
05:22 deafferret he got me on a roll. If nothing else, I have momentum.  :)
05:22 rbuels 9.
05:22 rbuels hours.
05:22 deafferret ya. burned 2 hours of no pay on that. -shrug-
05:23 deafferret but now I've done my first Ensembl API, so thats cool
05:24 rbuels true, you did at least get some knowledge out of it
05:24 rbuels where is that guy at?  he owes you like 20 beers and the indentured servitude of his firstborn
05:25 * rbuels looks at the backscroll
05:27 deafferret uci.edu
05:28 rbuels ah thanks, i had only gotten through about 2 hours of it up to then
05:28 rbuels lol
05:28 deafferret 21:35 -!- Emos [n=chatzill@dhcp-077c-201.bic.uci.edu] has quit
05:28 rbuels ah, there.
05:28 rbuels well at least he's burning the midnight oil
05:28 rbuels he'd better get himself a camel book
05:29 deafferret i'm glad to give back one millionth of the open source I've received  :)
05:29 rbuels so how many extra modules did he have to install there...
05:29 * rbuels greps for cpan
05:30 rbuels Bio::ASN1::Garbage and DBD::mysql i think
05:30 rbuels you know what's funny?
05:30 rbuels there's actually a CXGN::Garbage namespace in our ball of mud
05:32 rbuels what.  the.
05:32 rbuels google chrome os
05:32 rbuels http://www.nytimes.com/2009/07/08/t​echnology/companies/08operate.html
05:33 deafferret sorry, my brain's done for today. 00:33 here
05:33 rbuels heh OK
05:33 deafferret watching The Wire, then bed  :)
05:33 rbuels night
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