[galaxy-dev] tool_dependencies.xml Environmental Variable Question

variables are not available during runtime. Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotter

Re: [galaxy-dev] Plugins

Carl, Is there a way for a tool_shed installed tool to provide a plugin? Also, have you actually added any hooks anywhere? If so, where are they documented? Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA

Re: [galaxy-dev] Workflows with Conditionals and Loops

, Mar 5, 2014 at 9:05 PM, Michael E. Cotterell mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) wrote: Is there a way to have conditionals and loops for the various steps in a Galaxy workflow? For example, a conditional might be used to branch to various steps based

Re: [galaxy-dev] Workflows with Conditionals and Loops

and level of asynchrony. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter

Re: [galaxy-dev] Workflows with Conditionals and Loops

. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu

[galaxy-dev] Workflows with Conditionals and Loops

. Sometimes, this operation/step will inform us that the results are not ready. We would like to be able to loop on that second operation/step until it says the job is done, and then move on to a third operation/step to actually get the results. Any ideas? Sincerely, Michael E. Cotterell Ph.D

Re: [galaxy-dev] Plugins

is really eating up my time. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter

[galaxy-dev] Dynamically Generated Tools

not the recommended course of action, then I'd like some advice on what to do? Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Faculty Liaison, CS Graduate Student Association

Re: [galaxy-dev] Dynamically Generated Tools

Ross, Thanks for the comments. I've already made my main tool tool_shed compatible. What I'm wondering about is what do I do with the tools that my tool creates? Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA

[galaxy-dev] Java JAXB for Tool Configuration Files

to an XML schema definition (now I'm ranting :P). If one already exists, then all the better! Anyway, let me know if there's any interest. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Faculty

Re: [galaxy-dev] Dynamically Generated Tools

. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu

[galaxy-dev] Plugins

be figuring out where you want to place the hooks and documenting them for plugin developers. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Faculty Liaison, CS Graduate Student Association

Re: [galaxy-dev] Plugins

James, That's exactly what I was thinking. In my opinion, hooks are the way to go (as seen in my example), but if there's a better way then I'm game for that to. I just want to be able to extend Galaxy without modifying Galaxy itself. Thanks! Sincerely, Michael E. Cotterell Ph.D. Student

[galaxy-dev] virtualenv, jpype, and tool_dependencies.xml

/web_service_tools/65a0d7bb35d6/requirements.txt (line 1)) Storing complete log in /home/mepcotterell/.pip/pip.log Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Faculty Liaison, CS Graduate

[galaxy-dev] Installation Instructions slightly wrong

Just wanted to mention that the Get the latest copy [..] section at http://wiki.galaxyproject.org/Admin/Get%20Galaxy should have the user cd into galaxy-dist before performing hg update stable. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor

Re: [galaxy-dev] Tool Visibility

Any ideas? Thanks! On Monday, June 3, 2013 at 10:17 AM, Michael E. Cotterell wrote: Suppose a tool didn't have any kind of configuration and therefore didn't need to be displayed in the Analyze Data part of Galaxy. Is there a way to modify tool_conf.xml so that a particular tool is only

Re: [galaxy-dev] Tool Visibility

, it is designed to add tools to Galaxy itself. Perhaps there is a way to work this into the Toolshed stuff you guys are working on? Any thoughts are much appreciated. Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA

Re: [galaxy-dev] Tool Visibility

This is great! Will it work with sections as well? Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc

Re: [galaxy-dev] Tool Visibility

! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) http

Re: [galaxy-dev] Tool Visibility

Excellent. Is there an example of a modified universe_wsgi.ini file like the one mentioned in the description of the pull request? Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia mepcotter

[galaxy-dev] Tool Visibility

Suppose a tool didn't have any kind of configuration and therefore didn't need to be displayed in the Analyze Data part of Galaxy. Is there a way to modify tool_conf.xml so that a particular tool is only displayed in the Workflow editor? Thanks! Sincerely, Michael E. Cotterell Ph.D

[galaxy-dev] Feature Request - Reload Button

want some way of warning an admin if jobs are currently being executed. Thanks. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc

[galaxy-dev] nginx Proxy to VM problem

(thus avoiding the prefix issue), but for now I'm totally lost as to why I'm not able to login using my current configuration. Any ideas? Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University

Re: [galaxy-dev] nginx Proxy to VM problem

I actually fixed the problem by not setting the cookie prefix in the ini file. Weird. Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com

Re: [galaxy-dev] nginx Proxy to VM problem

That's not the only thing I changed. I also have the following in my nginx conf file: proxy_set_header Host $host; instead of X-Forwarded-Host $host Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University