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naturalis / supersmart

Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa
MIT License
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parse error in `smrt-utils plot` #87

Open hettling opened 9 years ago

hettling commented 9 years ago

Trying to visualize this tree with default parameters (smrt-utils plot), I am getting the error:

file error - parse error - /Users/hettling/git/supersmart/data/VISUALIZATION/supersmart.tmpl line 13: unexpected token (.)
  [% INSERT jquery-2.1.4.min.js %]

Other examples gibe the same error, and I cannot figure out what the problem is.

rvosa commented 9 years ago

Maybe the file name in the insert statement need to be quoted to escape the periods? I think it is trying to interpret them as method calls - though I hadn't seen this error previously....

On Mon, Nov 9, 2015 at 11:11 PM, hettling notifications@github.com wrote:

Trying to visualize this https://raw.githubusercontent.com/naturalis/supersmart/master/examples/primates/final.nex tree with default parameters (smrt-utils plot), I am getting the error:

file error - parse error - /Users/hettling/git/supersmart/data/VISUALIZATION/supersmart.tmpl line 13: unexpected token (.) [% INSERT jquery-2.1.4.min.js %]

Other examples gibe the same error, and I cannot figure out what the problem is.

— Reply to this email directly or view it on GitHub https://github.com/naturalis/supersmart/issues/87.

hettling commented 9 years ago

Commit 10d90fc64bcdbae515309ce8fdcd7c7ab44f0d1f stops errors and smrt-utils plot produces output. However, when I open the generated html in my Browser, I get a blank page...

hettling commented 9 years ago

Clades with marker files are now checked into the examples directory: https://github.com/naturalis/supersmart/tree/master/examples/primates. From there I call smrt-utils plot with output supersmart.html which does not show in my browser.

rvosa commented 9 years ago

So there is an inconsistency between the tree that is in that folder and the marker tables: the tables, both for the backbone and in several clades, contain taxa that are not in 'final.nex' (apparently due to #88)