Re: [galaxy-dev] Several jobs stalled in the queue: Job runner assigned but no external ID recorded

Hi guys, My list of the stalled jobs is getting longer and longer. Is there a fix of this? Cheers, Derrick On Sat, Jun 15, 2013 at 3:36 PM, Derrick Lin wrote: > Hi guys, > > I have several jobs have been stuck in the queue for long time, I checked > the handler log and found the following messa

[galaxy-dev] igv integration

I’m having some trouble with igv integration… it works fine for hg19, but for other this influenza genome i just added, i’m seeing from IGV [cid:9C974C45-560B-46C3-AF75-CC794D0D1ACD@neb.com] Any idea what I’m doing wrong? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Developme

[galaxy-dev] running tools within tool

Hi, This is a question I posted to galaxy user mailing list a while back and was redirected to dev for possible answers: Is it possible in Galaxy to design a tool whose sole purpose is to run other tools. This is motivated by our desire to enhance execution capabilities of existing tools via a gen

Re: [galaxy-dev] Cluster nodes without NFS access to galaxy-dev.

Hello Luca, This is an active area of development for the core team. It is fairly ingrained in Galaxy that workers and the the web server share a networked file system - so this is a real challenge. I would review the following recent thread: http://dev.list.galaxyproject.org/Managing-Data-Loca

[galaxy-dev] Running tools from within a tool

Hi, This is a question I posted to galaxy user mailing list a while back and was redirected to dev for possible answers: Is it possible in Galaxy to design a tool whose sole purpose is to run other tools. This is motivated by our desire to enhance execution capabilities of existing tools via a gen

Re: [galaxy-dev] Upload via FTP - Assertion Error on Change ownership of working dictory

Thanks for the tip Eric. I was able to figure it out. The key to this, was you suggested was permission issue. I had to modify sudoers so tty was not required. This will allow scripts to change ownership to the correct user so SGE can submit them. Thanks! -Adam -- Adam Brenner Computer Science,

[galaxy-dev] tools fails only in workflow

Dear all, I developed a tool which allows an optional selection as input amongst others. It works quite neat if I run it via "Analyse Data". Actually, it only breaks in one condition: If I try to run it "as a Workflow" and set the "multiple selection input" to be set at runtime AND do not sele

Re: [galaxy-dev] Cheetah code issue

That did the trick! Thanks! On Tue, Feb 4, 2014 at 10:26 AM, bjoern.gruen...@googlemail.com < bjoern.gruen...@gmail.com> wrote: > Hi, > > to access variables in a conditional you need to write something like that: > > $rangeorlist.rngstart > $rangeorlist.rend > $rangeorlist.stepsize > > Cheers,

Re: [galaxy-dev] Cheetah code issue

Hi, to access variables in a conditional you need to write something like that: $rangeorlist.rngstart $rangeorlist.rend $rangeorlist.stepsize Cheers, Bjoern 2014-02-04 Ketan Maheshwari : > Hi, > > While developing a tool, I am facing Cheetah code issue. I looked up the > mailing list archive

Re: [galaxy-dev] IGV display_application configuration failed with require_login=TRUE

On 04/02/2014 16:37, navratil wrote: Dear galaxy-dev team, We have configured a galaxy-dist server (stable release) behind an Apache2 proxy (with mod_xsendfile) by following the galaxy wiki. We would like to use the galaxy embeded user authentification with require_login=True option instead

[galaxy-dev] Cheetah code issue

Hi, While developing a tool, I am facing Cheetah code issue. I looked up the mailing list archive and found many similar issues reported earlier but could not debug this. Any tips in debugging is appreciated. File "cheetah_DynamicallyCompiledCheetahTemplate_1391530084_29_71368.py", line 97, in re

Re: [galaxy-dev] IGV display_application configuration failed with require_login=TRUE

Hi Vincent, I think there was an error that was fixed recently. If you can, please try yo upgrade or wait a few more days until the new galaxy-dist version is released. Bjoern 2014-02-04 navratil : > Dear galaxy-dev team, > > We have configured a galaxy-dist server (stable release) behind an

[galaxy-dev] IGV display_application configuration failed with require_login=TRUE

Dear galaxy-dev team, We have configured a galaxy-dist server (stable release) behind an Apache2 proxy (with mod_xsendfile) by following the galaxy wiki. We would like to use the galaxy embeded user authentification with require_login=True option instead of a remote_user configuration on the

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

Hi Peter, I've created the following Trello card for this. I know what the problems are, but I won't have time to get fixes for them for a while. Please continue to reposrt issues you discover and I'll make sure to get fixes as soon as I get time. https://trello.com/c/M1rwVWhI/143-nightly-te

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

Hi Peter, I've created the following Trello card for this. I know what the problems are, but I won't have time to get fixes for them for a while. Please continue to reposrt issues you discover and I'll make sure to get fixes as soon as I get time. https://trello.com/c/M1rwVWhI/143-nightly-te