Tim O'Donnell

Good question. We don't try to copy and source over to the worker currently. That seems error prone to me to try to do in general, but if you know...

Thinking of something like this: ``` name,command,input_files,output_files run1,wc -l $1 > result.txt,/path/to/some/text/file.txt,result.txt run2,wc -l $1 > result.txt,/path/to/another/text/file.txt,result.txt ``` Can discuss in person

The result from running the above would be a directory with `run1/result.txt` and `run2/result.txt`

Tried lowering the versions of google-api-python-client and oauth2client but hit a number of new issues involving unicode encoding and pickling, so for the time being leaving it as ``` "oauth2client==4.0.0",...

UCSC's has a huge number of possible tracks, and supports loading tracks directly from third party servers using their ["track hubs"](http://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html) ([examples](http://genome.ucsc.edu/cgi-bin/hgHubConnect)). My understanding, though I'm not 100% sure, is...

An important case for me is visualizing an arbitrary number of BAMs at once, as in IGV. On Tue, May 19, 2015 at 5:11 PM, Jeff Hammerbacher wrote: > >...

Cool. I'll throw out another idea I've been thinking of surrounding this; maybe it also lines up with something you've been thinking. I think the "run" concept may be limiting....

Gotcha. My main point is that we should consider having our "project specification" be useable by other tools like biokepi or Guacamole in addition to Cycledash. For example, I'd like...

Tracking the provenance of generated datasets using the Ketrew DAG could be useful, but is separate from what I'm thinking. I'm imagining a way to associate reads, variants, and other...

I was using UCSC's "variant annotation integrator" http://www.noncode.org/cgi-bin/hgVai On Tue, Feb 10, 2015 at 3:53 PM, Tavi Nathanson [email protected] wrote: > Consider adding more annotation information, depending on the direction...