Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-11-19

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All times shown according to UTC.

Time Nick Message
02:03 towodo joined #opentreeoflife
05:20 mtholder joined #opentreeoflife
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12:05 kcranstn joined #opentreeoflife
12:50 kcranstn @mtholder - you there?
12:50 mtholder yes
12:50 kcranstn trying to count total number of trees in phylesystem, but can’t figure out what to grep in the files
12:52 mtholder grep could be tough.
12:52 kcranstn better suggestions welcome
12:53 mtholder one sec... I'm on a branch in peyotl...
12:58 mtholder I have to drop off for a few minutes, but I'll send you a peyotl script (or put it in the repo) soon...
12:58 kcranstn great, thanks!
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13:44 towodo joined #opentreeoflife
14:14 mtholder kcranston: https://github.com/OpenTreeOfLife/peyotl/blob/master/examples/phylesystem/count_trees.py
14:16 mtholder The stats are:
14:16 mtholder 2913 = # studies
14:16 mtholder 183 = # studies without any trees
14:16 mtholder 6612 = # trees total
14:16 mtholder 61 = maximum # trees in any study (pg_2607)
16:52 kcranstn joined #opentreeoflife
16:53 kcranstn Putting together a figure for the paper, and wondering how I can get 1. the number of OTUs descended from a specific higher taxa in OTT; 2. the number of phylogenetically-supported tips in a specific clade of the synthetic tree
16:54 mtholder joined #opentreeoflife
17:21 towodo kcranstn, 1. is pretty easy using smasher
17:22 towodo tax = getTaxonomy(…); tax.taxon(‘Aves’).count()    or something close to that
17:22 kcranstn excellent, thanks
17:23 towodo not sure of the exact method name. it might be documented, or else I’d check Taxon.java
17:23 towodo tax = getTaxonomy(‘ott2.8/‘)
17:24 towodo after downloading ott2.8
17:27 towodo yes, the method is .count()
17:27 kcranstn I think we need better documentation in the readme about running Smasher. I am not sure how to “run Smasher"
17:33 kcranstn i.e. I am sitting in the reference-taxonomy repo, but not sure what to do next
18:00 towodo hmm
18:01 kcranstn now I am in java installation hell
18:01 towodo I was thinking https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/doc/scripting.md
18:01 towodo oh no…
18:01 towodo smasher can use any version 1.6 or later
18:01 towodo maybe even 1.5
18:01 kcranstn I am going to put a link from the readme to that docs dir
18:01 kcranstn didn’t look there
18:01 towodo I understand why not
18:02 towodo you’re on a mac, yes? and have tried to do an oracle JDK install? (not just JRE)
18:03 towodo I agree that it’s hell, but it’s not hell like Dryad SWORD hell
18:04 towodo I vaguely remember some sort of java installation hell from this summer
18:04 towodo oracle wants you to register. and the list of links provided is not in recognizable terms
18:07 towodo I am going to get some lunch… back in a bit
18:41 towodo back
18:41 kcranstn going better now. Have run make aster successfully
18:47 kcranstn from org.opentreeoflife.smasher import Taxon = good
18:47 kcranstn from org.opentreeoflife.smasher import Taxonomy = fail
18:48 kcranstn java.lang.NoClassDefFoundError: java.lang.NoClassDefFoundError: org/json/simple/parser/ParseException
19:13 kcranstn ok, stephen can get me the numbers from treemachine
19:46 towodo cannot reproduce.  works for me
19:47 towodo there was a cert problem for jython, which I patched by adding —no-check-certificates
19:48 towodo but then it went fine
19:48 towodo kcranstn ^
19:48 kcranstn hmmm...
19:48 kcranstn I am giving up, since stephen can get the ott numbers, and I need other stats from treemachine anyway
19:49 towodo stephen’s numbers do not include incertae sedis (about 30% of taxa)
19:49 towodo fyi
19:49 kcranstn argh
19:49 towodo send me a list of taxa and i can get you the counts
19:49 kcranstn I’ll just be clear about that in the text for the figure
20:20 towodo see email… gotta skeedaddle, sorry, back online this evening
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