Re: [galaxy-dev] Data manager .loc file not installing in correct place

Hi Daniel, Thank you for your response! I tried this again and this time it worked just fine. It appears the weird file is garbage collected after a while or when the galaxy server is restarted. Thanks again! Jeremy Liu jeremy@yale.edu On Tue, Jan 13, 2015 at 2:35 PM, Daniel Blankenberg wro

Re: [galaxy-dev] LD_LIBRARY_PATH not exporting to galaxy

Well we are using the "environment_setup_file" option in our galaxy.ini file. Supposedly we can point to a shell script that will be sourced before running each job. In this script we load all of the environment variables using modules. The paths are all correct after this runs. However, the python

[galaxy-dev] GalaxyAdmins Online Meetup on 19 February

Hello all, The first GalaxyAdmins meetup of 2015 will happen online on Thursday, 19 February . GalaxyAdmins

Re: [galaxy-dev] Starting uWSGI

On Wed, Jan 28, 2015 at 11:55 AM, Nicholas Kline wrote: > Hi Nate. Thank you for the reply. So I installed uWSGI inside my > Python virtual environment since that was one of the options listed in > the documentation, like so: > > cd ~/galaxy_env/ > source bin/activate > pip install uw

Re: [galaxy-dev] Starting uWSGI

Hi Nate. Thank you for the reply. So I installed uWSGI inside my Python virtual environment since that was one of the options listed in the documentation, like so: cd ~/galaxy_env/ source bin/activate pip install uwsgi It looks like uWSGI was successfully installed. I then exited/deac

Re: [galaxy-dev] data collections - workflow - bug?

I will try to build a smaller testcase that fails and talk about the job handlers with Björn tomorrow. I tried this with quite a big workflow which I built from scratch (in the editor). I'll get back to you. Best, Torsten On 27.01.2015 18:25, John Chilton wrote: Sorry again about this mixup

Re: [galaxy-dev] NFS configuration questions + NFS /etc/fstab configuration issue with AMI issue

Hey Scott, Glad you figured out the other two issues. Which file exactly are you editing that is getting overwritten? And when does it get overwritten? (on reboot, randomly, cluster terminate/start, etc?) -Dannon On Sun Jan 25 2015 at 12:20:12 PM Scott Jeschonek wrote: > Revising all of the

Re: [galaxy-dev] LD_LIBRARY_PATH not exporting to galaxy

Hi Nik, Is there any chance that $LD_LIBRARY_PATH is being set in the parent shell but not exported? --nate On Wed, Jan 28, 2015 at 7:04 AM, Nikhil Joshi wrote: > To answer your questions from above, in case it can help with this new > problem, we are sourcing the modules from an "env.sh" scri

Re: [galaxy-dev] LD_LIBRARY_PATH not exporting to galaxy

To answer your questions from above, in case it can help with this new problem, we are sourcing the modules from an "env.sh" script whose full path is the value of the "environment_setup_file" option. This fixed our first problem, but not this second one. We created the modules ourselves for each o