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I was following the instructions in the wiki and was totally unprepared for the following:
bash-3.2$ j inittaxsyn ncbi example/nematoda.ncbi /dev/null nem.db
taxomachine version alpha.alpha.prealpha…
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There should be a way to look at the lineage, along with the incertae sedis status of any link in the lineage. (Maybe all flags, I don't know - at least the ones related to taxa included by taxomachin…
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This looks like someone mistakenly checked in work in progress. There are no packages of the form "org.opentree".
[INFO] --- maven-compiler-plugin:2.5:compile (default-compile) @ opentree-neo4j-plug…
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github.com/nmatasci/TNRS.git
or github.com/iPlantCollaborativeOpenSource/TNRS.git ?
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seems like content_rootnode_ottol_id is returning the node id and not the ottol id. needs to be the ottol id. uid's returned for matches appear to be correct
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we need to be able to deal with these before they are added to the graph. The idea would be to
- TNRS the names that are there using taxomachine
- For ones that match that weren't matched before, w…
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It is necessary to have to context ottol id for adding new taxa from phylografter.
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Bio-Phylo-0.55 fails its tests when SVG.pm is installed with perl-5.18.0 from perlbrew on Mageia Linux Cauldron x86-64. Here is the shell session. Please look into fixing it.
``` text
shlomif@telaviv…
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We seem to just be composing JSON by hand, which is typically easy. We could use something like: http://jettison.codehaus.org/apidocs/org/codehaus/jettison/json/JSONStringer.html
In many cases we kn…