Camelia, the Perl 6 bug

IRC log for #bioruby, 2013-04-22

| Channels | #bioruby index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
00:14 agarie joined #bioruby
00:50 rgirish28 joined #bioruby
02:35 shevy joined #bioruby
03:00 rgirish28 joined #bioruby
03:31 rgirish28 joined #bioruby
03:38 robsyme joined #bioruby
05:05 rgirish28 joined #bioruby
05:10 rgirish28 joined #bioruby
05:17 george__ joined #bioruby
05:41 george__ joined #bioruby
05:57 pjotrp joined #bioruby
06:28 george__ joined #bioruby
08:32 ilpuccio joined #bioruby
08:38 ilpuccio joined #bioruby
09:05 arrigoni joined #bioruby
10:06 ilpuccio I have a lot of troubles installing gems under ruby 2.0 with newest ruby gem, sob
10:52 arrigoni joined #bioruby
11:36 george__ joined #bioruby
11:43 george__ is there an inbuilt approach to creating fastq files?
11:44 george__ there an internal FASTQ parser Bio::Fastq. But i do not find an expressive method/function for creating fastq. I could be missing something :)
11:49 pjotrp ilpuccio: why upgrade?
11:50 pjotrp george__:  we are better at writing parsers ;)
11:50 ilpuccio just because 2.0 is the new stable
11:50 pjotrp not that stable for gems :)
11:51 pjotrp I don't know why they insist on breaking things
11:51 ilpuccio that's what hurts me every time, lack of compatibility it seems that they do not care ...
11:51 pjotrp proc vs lambda comes to mind
11:52 pjotrp it is clear they don't care. Maybe rightfully so, but still
11:54 george__ @pj would be nice to extend the bio::sequence class to accept quals and add a to_fastq method?
11:56 ilpuccio george__, if i remember correctly we discussed this stuff years ago but… in the end … if you have millions of sequences the fastest way is to process them without a real parser
11:56 ilpuccio obviously depends on your goal
12:01 rgirish28 joined #bioruby
12:06 george__ it might still be useful if dealing with a few thousand sequences .. just for convinience
12:07 arrigoni joined #bioruby
12:14 ilpuccio george__, sure
12:15 ilpuccio could someone try to install bio under ruby 2.0 ?
12:20 ilpuccio maybe it's my computer but I can not get rid of RVM and Ruby in these days
12:23 robsyme left #bioruby
12:33 ilpuccio i get this error https://gist.github.com/helios/5434576
12:34 george__ I have bio under 2.0
12:34 george__ did not get any issues during installation
12:40 ilpuccio george__, thanks
12:45 george__ am using rbenv to manage the rubies. dont know if it could be a factor
12:47 ilpuccio george__, maybe rbenv work I had only a problem with different version of rake , jot asked me to overwrite the latest version with an old one (rake mean)
13:03 pjotrp rvm, rbenv, chruby - all attempts at replacing real package management
13:03 rgirish28 joined #bioruby
13:05 rgirish28 joined #bioruby
13:09 ilpuccio pjotrp, so ? we need that stuff to manage different installation… maybe are my computers that are screwed
13:13 ilpuccio I'm just saying that are useful if you want to have a mixed environment
13:35 ilpuccio no way I can not make it work with 2.0
14:14 rgirish28 joined #bioruby
14:18 george__ joined #bioruby
14:35 pjotrp ilpuccio:  strange
14:36 pjotrp If I had to manage heterogeneous environments I would use nixpkgs
14:36 ilpuccio now I'm using 1.9.3 I want to fix all the bugs for biogem and then move the code base to 2.0
14:36 pjotrp A bit of learning curve, and no looking back
14:36 pjotrp Cool
14:43 pjotrp ilpuccio:  I need to fix a few more things with the website. Thereafter I'll pay some attention to biogem too.
14:54 pjotrp in between jobs, holidays and conferences...
15:11 ilpuccio i must leave but there are so many changes in jeweler I'll try to do my best to fix it.
15:11 ilpuccio see ya
16:12 george_ joined #bioruby
18:38 george_ joined #bioruby
18:58 rgirish28 joined #bioruby
19:01 agarie joined #bioruby
19:01 rgirish28 joined #bioruby
19:21 fstrozzi joined #bioruby
19:48 arrigoni joined #bioruby
21:51 ilpuccio joined #bioruby

| Channels | #bioruby index | Today | | Search | Google Search | Plain-Text | summary