[galaxy-dev] "Could not save visualization" error with "June 23, 2011" release

Hi I am pretty sure, this must have been discussed before, but again, I cannot find a hint/reference in the e-mail archive: If I install a new galaxy server using the "June 23, 2011" release (changeset: 5743:720455407d1c), I cannot save a visualization after adding a new track: I get a l

Re: [galaxy-dev] "Could not save visualization" error with "June 23, 2011" release

Hi Hans, > Is this a 'bug' in the "June 23, 2011" release ? Probably. > By looking through the commits on galaxy central i found the 'changeset: > 5750:b13d16085dfc' from Jun 27: "Add generic method for getting track type > and use it when saving visualizations." > > I am now using the two '

Re: [galaxy-dev] Handling runner-specific (SLURM) DRMAA settings (Roman Valls)

Hey Nate, On 2011-08-16 20:21, Nate Coraor wrote: > Roman Valls wrote: >> Thanks indeed for the ~/.slurm_drmaa.conf hint Mariusz, very useful ! >> >> I wonder how this approach will work out when one runs galaxy as advised >> in a production setting: >> >> http://usegalaxy.org/production >> >> To

[galaxy-dev] Using data_fabfile.py to update data from s3

Hi, I am trying to use install_data_s3 (data_fabfile.py) to get data from the cloudbiolinux bucket into a virtualbox VM, as per the instructions at usegalaxy.org/vm . When I ran fab -f data_fabfile.py -H localhost install_data_s3:config/galaxy_default_biodata.yaml the first time, it worked. But

Re: [galaxy-dev] [galaxy-bugs] Some issues when running jobs through drmaa job runner.

On 2011-08-16 23:49, Luobin Yang wrote: > Hi, Nate, > > On Tue, Aug 16, 2011 at 12:38 PM, Nate Coraor > wrote: > > Hi Luobin, > > Sorry for the delay in response. I would suggest moving this discussion > to the galaxy-dev mailing list since it does not conta

Re: [galaxy-dev] [galaxy-bugs] Some issues when running jobs through drmaa job runner.

On Wed, Aug 17, 2011 at 2:59 AM, Roman Valls wrote: > On 2011-08-16 23:49, Luobin Yang wrote: > > Hi, Nate, > > > > On Tue, Aug 16, 2011 at 12:38 PM, Nate Coraor > > wrote: > > > > Hi Luobin, > > > > Sorry for the delay in response. I would suggest moving this >

Re: [galaxy-dev] [galaxy-user] tailoring backend SGE submission requests to specific applications

Joseph Hargitai wrote: > > Hi, > > is there a best practices, to replace general SGE requests with requests > specific to applications - Hi Joe, I've moved this question to the dev list since it concerns a local installation. You can tailor SGE options per-tool as shown at the bottom of the p

[galaxy-dev] latest checkout (today) does not have Help or User

Hi, built a new server today to test a few things. a, Help is not clickable via Apache2 proxy 2, when you use an apache2 proxy is it for granted that local authentication cannot be used? I tired remote-user = False hoping i can use load-balancing and proxy but retain local authentication. But

Re: [galaxy-dev] Handling runner-specific (SLURM) DRMAA settings (Roman Valls)

Roman Valls wrote: > Hey Nate, > > > On 2011-08-16 20:21, Nate Coraor wrote: > > Roman Valls wrote: > >> Thanks indeed for the ~/.slurm_drmaa.conf hint Mariusz, very useful ! > >> > >> I wonder how this approach will work out when one runs galaxy as advised > >> in a production setting: > >> > >>

[galaxy-dev] Modifying how runtime inputs are resolved when running a workflow

This is probably something only the Galaxy devs can answer, but I thought I'd give it a shot in the wider community. Some of you are doing some very complicated stuff. If you have a workflow with several input blocks, you might have multiple fastq files you need to provide. A good example of th

Re: [galaxy-dev] Using data_fabfile.py to update data from s3

Clare; > I am trying to use install_data_s3 (data_fabfile.py) to get data from > the cloudbiolinux bucket into a virtualbox VM, as per the instructions > at usegalaxy.org/vm . > > When I ran > fab -f data_fabfile.py -H localhost > install_data_s3:config/galaxy_default_biodata.yaml > the first tim