Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-04-17

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All times shown according to UTC.

Time Nick Message
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00:00 travis-ci OpenTreeOfLife/phylesystem-api#727 (support-tree-collections - 8490b77 : Jim Allman): The build passed.
00:00 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/25892310c706...8490b77f3994
00:00 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/58840192
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00:03 travis-ci OpenTreeOfLife/phylesystem-api#728 (support-tree-collections - 99a4aee : Jim Allman): The build passed.
00:03 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/8490b77f3994...99a4aeefcf22
00:03 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/58840372
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00:08 travis-ci OpenTreeOfLife/phylesystem-api#729 (support-tree-collections - c66237c : Jim Allman): The build passed.
00:08 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/99a4aeefcf22...c66237cb1efb
00:08 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/58840974
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14:16 josephwb hey mtholder
14:16 josephwb you running this supertree stuff on mac?
14:17 kcranstn linux
14:18 josephwb r u sure?
14:18 josephwb clang seems to be the defaulty
14:18 josephwb and i am getting sed problems on linux
14:18 josephwb i know mac (annoyingly!!!) uses a different sed
14:30 mtholder sorry I'm here.
14:30 mtholder ubuntu
14:30 mtholder josephwb ^
14:31 mtholder odd. I'm having a prob too, standby...
14:31 josephwb i can't get this working at all...
14:31 josephwb probably me being an idiot
14:31 josephwb i fixed a bunch of shell commands in various readmes
14:32 mtholder just fixed the sed thing and pushed.
14:32 josephwb ok, will try
14:33 josephwb making it a bit further now
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14:34 mtholder thanks for fixing the typos in the refs to your repo.  I actually have them in a different spot on my machine. So what is the readme is my recreation of the commands that I used for a more generic audience. 'course that means I added typos...
14:35 josephwb currently:
14:35 josephwb make: *** No rule to make target 'step_4/step-5-phylo-args.txt', needed by 'step_5/taxonomy.tre'.  Stop.
14:36 josephwb is:
14:36 josephwb 'step_4/step-5-phylo-args.tx
14:36 josephwb correct?
14:36 josephwb maybe:
14:36 josephwb step_5/step-5-phylo-args.txt
14:36 josephwb ?
14:37 mtholder yeah - i just pushed that.
14:37 mtholder old name (so it was on my machine, which is why it worked for me)
14:38 josephwb otc-nonterminals-to-exemplars -estep_5 step_1/taxonomy.tre -fstep_4/step-5-phylo-args.txt
14:38 josephwb terminate called after throwing an instance of 'otc::OTCError'
14:38 josephwb what():  Could not open file "step_4/step-5-phylo-args.txt"
14:38 josephwb Makefile:57: recipe for target 'step_5/taxonomy.tre' failed
14:38 josephwb make: *** [step_5/taxonomy.tre] Aborted
14:38 josephwb i think you missed one in the makefile
14:38 josephwb line 57
14:38 mtholder you are correct.
14:38 josephwb it's going!
14:38 josephwb (i think...)
14:39 josephwb want me to push, or you?
14:39 mtholder i pushed. thanks.
14:39 josephwb ok
14:43 josephwb ok, crashed at the expected spot. wee.
14:43 josephwb thanks for helping me sort that out
14:43 mtholder sure. thanks for fixing the issues w/ reames and makefiles
14:45 josephwb so subprobs in: step_7_scratch/export-sub-temp
14:45 mtholder yes
14:46 mtholder should be identical to the ones that I posted
14:47 josephwb same number
14:50 mtholder in the "exemplar for tips mapped to higher taxon" step, the leftmost tip that descends from the non-terminal taxon is chosen as the exemplar (when the taxon is not represented by any other tree). So that step is sensitive to branch rotation in the taxonomy. but otherwise, things should be deterministic and invariant to different newick represenations of the same tree.
14:51 mtholder in other words: there is no randomness in the routine.
14:52 josephwb ok
14:53 josephwb using same taxonomy file
14:57 josephwb far fewer subproblems
14:57 mtholder than what I posted? or before?
14:57 josephwb 5723 -> 5381
14:57 josephwb from before
14:57 mtholder yes.
14:57 josephwb same as you posted (we throw out taxonomy-only ones)
14:58 mtholder before a tip mapped to a higher taxon caused all of the taxonomic children to be emitted.
14:58 mtholder many of those resulted in taxonomy only problems
14:58 mtholder that we can graft onto the tree later.
14:59 mtholder the exemplar approach reduces the incidence of taxonomy only problems.
15:00 josephwb i like the commit message "same typo different line"
15:01 mtholder I should have a bash alias for that.
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