Camelia, the Perl 6 bug

IRC log for #bioperl, 2012-02-07

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

All times shown according to UTC.

Time Nick Message
11:46 leont joined #bioperl
12:29 zenman joined #bioperl
12:38 cap1 joined #bioperl
12:46 carandraug joined #bioperl
12:53 carandraug joined #bioperl
17:45 scottcain joined #bioperl
19:50 awwaiid joined #bioperl
19:50 awwaiid hello genehack!
20:02 genehack hey awwaiid
20:03 awwaiid do you always hang out here, or did you just come to harass people like I did?
20:03 genehack no, i lurk here, mainly for hysterical raisins
20:04 awwaiid yummy
20:04 genehack and to harass deafferret
20:06 * pyrimidine likes hysterical raisins
20:07 pyrimidine They have a lot in common with jumping beans, so I hear
20:07 * rbuels envisions loosing a basket full of cobras in a nudist retirement community
20:09 pyrimidine seems we're all lurking about today ;)
20:11 * rbuels wiggles back into the jungle hillside, smooths his coating of mud, and tucks his Ka-Bar out of sight behind his muscular thigh
20:12 * rbuels puts first blood part II in his netflix queue
20:50 sl33v3_ joined #bioperl
21:00 scottcain joined #bioperl
21:17 pyrimidine gah, scottcain left...
22:01 scottcain joined #bioperl
22:17 scottcain_ joined #bioperl
22:18 pyrimidine hey, scottcain, did casandra indicate she was trying to use local::lib?
22:18 scottcain In her original email, there was an attachment that had her cpan session, where she tried to install local::lib but it failed.
22:19 pyrimidine ah, missed that
22:19 scottcain No worries; Dave's directions are so much better for most people anyway.
22:20 pyrimidine yeah, but my worry is the reliance on bioperl-live, which will break severely at some point
22:22 * leont agrees with pyrimidine
22:23 leont cpan skills are something worthy to promote, it will make end users life easier. Odds of them not needing something from it at some point are slim IMO, YMMV
22:27 pyrimidine leont++
22:29 pyrimidine yes, this is a problem.  We're currently locked into helping users with very little CS experience (let alone perl experience), but I would rather direct them to doing things the perl way than the bioperl way
22:29 scottcain True--and users still need to get prereqs installed :-/
22:29 pyrimidine yep
22:30 pyrimidine just setting PERL5LIB sets us up for 'Why is Bio::Foo dying', with an obvious missing dependency issue
22:31 pyrimidine maybe we need a flowchart
22:32 pyrimidine if you are a biologist with no computational experience, start here
22:32 leont For them, a script that sets up local::lib may be useful
22:33 scottcain leont: yes, I would have thought the authors of local::lib would have already done that (but apparently not--I still don't use it, so I don't know much about it)
22:33 * leont knows the authors
22:34 leont (or at least most of them)
22:34 pyrimidine yes, something akin to what is used to set up cpanm, for instance:
22:34 pyrimidine curl -L http://cpanmin.us | perl - App::cpanminus
22:35 pyrimidine we could probably set something up off bioperl.org to help along those lines
22:36 pyrimidine .oO( could set up cpanm was well )
22:36 leont In general, cpanm is more noob-friendly
22:36 pyrimidine yeah, I agree
22:37 leont Recent versions of CPAN.pm are a lot better (less questions, better defaults), but they're not quite cpanm
22:38 pyrimidine cpanm forced them to make things easier
22:38 leont Actually, I think cpanm can bootstrap local::lib too
22:38 pyrimidine yep
22:39 pyrimidine https://metacpan.org/module/App::cpanmi​nus#Installing-to-local-perl-perlbrew-
22:39 pyrimidine just bootstrap w/o the sudo
22:39 scottcain So perhaps good newb directions for installing cpanm and bootstrapping local::lib in the process would likely do the trick.
22:39 pyrimidine yes, I think so
22:42 pyrimidine This could be generically documented on the wiki
22:42 * pyrimidine heading out
22:46 scottcain joined #bioperl
22:46 leont Also, PREFIX/--prefix should be removed from the wiki, it's a somewhat problematic feature that has been superseded with --install_base
22:47 pyrimidine leont: if you want, feel free to change that.  The installation docs are pretty stale
22:48 pyrimidine or we can mark this as a bug, just to make sure it gets addressed...
22:48 * pyrimidine has more on my plate these days that I used to :)
22:50 pyrimidine left #bioperl
22:50 pyrimidine joined #bioperl

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