Re: [galaxy-dev] Job submission failed

Hi Vipin Is this a new problem you encounter since you have done the upgrade to "latest_15.03"? If so, did you experience any troubles during the database schema upgrade to '128'? Regards, Hans-Rudolf On 04/20/2015 08:44 PM, Vipin TS wrote: Hi dev-team, I am experiencing an issue with m

Re: [galaxy-dev] Job submission failed

Another question is are there any logs indicating issues on the server side and can you open your web console and let us know if there are any errors reported there on the client side (e.g. https://developer.mozilla.org/en-US/docs/Tools/Web_Console). -John On Tue, Apr 21, 2015 at 3:45 AM, Hans-Ru

Re: [galaxy-dev] pbs/torque config

On Fri, Apr 17, 2015 at 3:26 PM, Beginner TI wrote: > Hi, > > I'm trying to enable the capability to submit jobs to a pbs cluster, however > I am quite confused by the documentation. I don't know where I could specify > the pbs server. I saw the following on the page: > > https://wiki.galaxyprojec

Re: [galaxy-dev] metadata in parallelization

Thanks for the report! I can confirm the bug and I opened a pull request with the fixes here https://github.com/galaxyproject/galaxy/pull/139. -John On Fri, Apr 17, 2015 at 4:20 AM, Roberto Alonso wrote: > Hello, > > I am writing some code to enable parallelization for some tool wrappers. > Firs

Re: [galaxy-dev] Serving a galaxy instance over Apache

This configuration looks correct - are you sure the correct properties are set in config/galaxy.ini: You need this section: [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy And [app:main] needs following properties: filter-with = proxy-prefix cookie_path = /galaxy I would al

Re: [galaxy-dev] Adding a dataset to a dataset list breaks "Run this job again"

Indeed - I can confirm this problem. Thanks a ton for the report! I have opened a pull request with a fix - https://github.com/galaxyproject/galaxy/pull/141 - sorry about that. -John On Wed, Apr 15, 2015 at 6:19 PM, Brian Claywell wrote: > While testing an upgrade from latest_2014.10.06 to GitH

[galaxy-dev] GCC2015 Registration and Lodging Scholarship for US-Based Post-Docs and Students

Hello all, *We are pleased to offer registration and lodging scholarships for GCC2015 for students and post-docs who are based in the United States, and who are members of historically underrepresented groups in

[galaxy-dev] Problem killing jobs (via Admin>Manage Jobs)

Hi all, I am having an issue killing jobs via Admin>Manage Jobs. When I try to submit kills I see this in the Galaxy log: galaxy.jobs.runners.local WARNING 2015-04-19 15:55:03,089 stop_job(): 10374: no PID in database for job, unable to stop I have updated my local Galaxy server (via hg) and a

Re: [galaxy-dev] Galaxy for Natural Language Processing

On Apr 15, 2015, at 5:35 AM, Björn Grüning wrote: > Nice! Can I convince you to put these tools into the TS if everything is > working? Maybe with a German beer? ;) Do you have a beer preference? We will definitely share our tools when they are stable, either on the public tool shed or we wi

[galaxy-dev] Issue writing functional tool test with repeat tag in config

Hello, I'm trying to format a test tag in a tool config for the public Tool Shed that includes a repeated input parameter. I followed the syntax suggested in the following archived galaxy-dev post (was unable to find much other guidance): http://git.net/galaxy-development-source-control/msg1524

Re: [galaxy-dev] Issue writing functional tool test with repeat tag in config

Hi CS, I assume you have the rest of the tags, but didn’t paste it here. One thing is that you need to close your test and tests elements properly: > > You may want to pass your config through a simple xml validator to try to shake any other issues out as well. Thanks for usi

Re: [galaxy-dev] Issue writing functional tool test with repeat tag in config

Thanks, Dan; the Tool Shed accepted the repo as a valid utility now (big oops on my part). I had to make a few other corrections to the wrapper script as well, so we’ll see how the automated tool testing goes… Do you know how often testing is conducted on the site? Thanks again, C On Apr 21, 2

Re: [galaxy-dev] Issue writing functional tool test with repeat tag in config

Christy, You may be interested in using planemo for local testing of tools, rather than waiting for the automated tool shed testing. http://planemo.readthedocs.org/en/latest/ http://planemo.readthedocs.org/en/latest/commands.html#test-command Cheers, Eric 2015-04-21 15:25 GMT-05:00 Christy Sha

Re: [galaxy-dev] Job submission failed

Hi Hans, Yes, this happened after upgrading to the version latest_15.03. The db upgrade was fine, didn't throw any error message to me. Thanks, Vipin On Tue, Apr 21, 2015 at 3:45 AM, Hans-Rudolf Hotz wrote: > Hi Vipin > > Is this a new problem you encounter since you have done the upgrade to

Re: [galaxy-dev] Job submission failed

Hi John, I am seeing an error in browser console when click on a tool link: POST https://galaxy.cbio.mskcc.org/api/tools 403 (Forbidden) " 403 Forbidden Forbidden You don't have permission to access /api/tools on this server. which points to the tool-jobs.js line #65, which is the error part