Re: [galaxy-dev] Tool test question

2012-07-18 Thread christopher fletez-brant
test XML look like? --nate On Sat, Jul 14, 2012 at 8:54 PM, christopher fletez-brant cafletezbr...@gmail.com wrote: Hi Nate, Thanks for the reply. Error messages are output at the bottom of the message. Setup is that the tool has a number of inputs, one of which is actually

Re: [galaxy-dev] Tool test question

2012-07-15 Thread christopher fletez-brant
- -- Ran 1 test in 16.540s FAILED (failures=1) On Thu, Jul 12, 2012 at 4:20 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 5, 2012, at 8:20 PM, christopher fletez-brant wrote: Dear Dev List, I am currently writing tests

[galaxy-dev] Tool test question

2012-07-06 Thread christopher fletez-brant
Dear Dev List, I am currently writing tests for a tool I am developing and am coming up short in understanding why it's failing. Using the test data, I can generate output identical to the output provided for testing every time I run the tool from my local Galaxy server. However, when I run the

[galaxy-dev] Python/R Script Not Integrating with Galaxy Correctly

2012-01-09 Thread Christopher Fletez-Brant
Hello Galaxy-Dev List, I am having some issues in getting a script to work correctly in Galaxy. My script is written in Python, uses RPy2 to pass some data to the R environment and then calls a custom R function; the output of this function, and of the greater Python/R tool, is a file. I am

[galaxy-dev] Script can't find other script

2012-01-05 Thread Christopher Fletez-Brant
Good afternoon Galaxy list, I've got a Python script which calls an R script. When I run a job using Galaxy, I get the following output from R: Error in file(file, r, encoding = encoding) : cannot open the connection In addition: Warning message: In file(file, r, encoding = encoding) :