[galaxy-dev] May 11, 2012 Galaxy Development News Brief

Dear Galaxy Community, The May 11, 2012 Galaxy Distribution has been released at: http://bitbucket.org/galaxy/galaxy-dist/ Complete News Brief *Highlights:* * *EMBOSS* tools and datatypes have now moved from the _/Galaxy distribution

Re: [galaxy-dev] Problem related to a job that "failed"

No I was not running it as user "galaxy" (was running it as me). I suppose I will have to request our sys administrator to run the command. So in general this would not be an end-user user accessible solution (easily) for us. We will try changing the "output_collection_parameter" as you had sug

Re: [galaxy-dev] Problem related to a job that "failed"

On May 11, 2012, at 4:18 PM, Kelkar, Hemant wrote: > No I did not execute it on the "galaxy" server. I do not have shell access to > the blade that actually runs the galaxy server. > So I would need to get my sys admin to run this then? Not necessarily, as long as you are running it as the same

Re: [galaxy-dev] Problem related to a job that "failed"

No I did not execute it on the "galaxy" server. I do not have shell access to the blade that actually runs the galaxy server. So I would need to get my sys admin to run this then? >That's pretty odd, you're executing this on the Galaxy server? What happens >if you run fetch_eggs.py in the sam

Re: [galaxy-dev] Problem related to a job that "failed"

On May 11, 2012, at 4:05 PM, Kelkar, Hemant wrote: > Thanks Nate for your prompt response. > > Here is what I tried. > > Got the jobid (e.g. 02b1cfb59f716d61) from the file download link (could not > find the "display URL" as you described). > > Then tried to use the helper script but got the

Re: [galaxy-dev] Problem related to a job that "failed"

Thanks Nate for your prompt response. Here is what I tried. Got the jobid (e.g. 02b1cfb59f716d61) from the file download link (could not find the "display URL" as you described). Then tried to use the helper script but got the following error: python ./helper.py -d 02b1cfb59f716d61 Traceback

Re: [galaxy-dev] Problem related to a job that "failed"

On May 11, 2012, at 3:39 PM, Kelkar, Hemant wrote: > All, > > This question pertains to a local galaxy install where the jobs are being > submitted to a cluster running LSF. > > I periodically get an error from a galaxy job (“Job output not returned from > cluster”) even though the job comp

[galaxy-dev] Problem related to a job that "failed"

All, This question pertains to a local galaxy install where the jobs are being submitted to a cluster running LSF. I periodically get an error from a galaxy job ("Job output not returned from cluster") even though the job completes properly on the cluster. In researching this issue our syst

Re: [galaxy-dev] Running Galaxy behind apache2

On May 10, 2012, at 4:23 PM, CHEBBI Mohamed Amine wrote: > Hi Galaxy team ; > I'am trying to put Galaxy into a production environment behind apache2 : > > I followed the tuto in http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy > for putting galaxy behind apache2 so I installed all the modu

Re: [galaxy-dev] About the creation of a new folder

On May 10, 2012, at 11:34 PM, Ciara Ledero wrote: > Hi all, > > I would just like to ask if it's possible to create a new folder (via script) > in the galaxy-dist folder. Hi Ciara, If you mean a new Data Library folder, then yes, via the API. If you mean a new subdirectory on the filesystem

Re: [galaxy-dev] ⇝ IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/base_panels.mako.py'

On May 10, 2012, at 6:59 PM, Luciano Cosme wrote: > > Hi Everyone, >I was just using my local galaxy instance. I closed it up (from terminal), > open IGV to look at some genes, then I restarted it from the terminal and > when I tried to access it I got the error message below. I just don't

[galaxy-dev] POST and WSGI

Hi, I am trying to set up Galaxy with an IdP. Yet, after the autentication, the SAML data coming via POST method to the WSGI (Galaxy) dissappears. I can only see it in a Firefox add-on, scrolling, but there is no way I can get hold of it in order to validate the users. Any idea how one can

Re: [galaxy-dev] [galaxy-user] default data for a tool

Hi, I would like to write my xmls in a way that reduces the amount of effort a casual guest user would require to try a tool from my local galaxy install. For example, in the remove_beginning tool I would like to set it up in a way that I could tell someone to do this: 1) go to the website that h

Re: [galaxy-dev] cloudman on ubuntu 12.04

I now see that there is already support for this in the current repo, but I was using the cm.tar.gz in the default cloudman bucket, which is older and doesn't have the ubuntu 12.04 support. My mistake, pretend you never saw it. cheers, jorrit On 05/11/2012 12:27 PM, Jorrit Boekel wrote: Dear

[galaxy-dev] cloudman on ubuntu 12.04

Dear list, I have tried to use cloudman on ubuntu 12.04 (with mi-deployment scripts). It didn't run very smooth. One of the issues seems to be that SGE depends on libc.so.6, which is not in the location where cloudman expects it. If not fixed yet, I'll create a pull request for the fix (two