[galaxy-dev] Galactic News!!! February 2015 Edition

Hello all, February brings lots of Galaxy related news , including events news : - *GCC2015: 6-8 July, Norwich UK

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

It is a regular system installation. Just for a sanity check, I checked the md5 hash with the same version of my local python and it is the same. Also, as a sanity check, I ran the tests on my local machine and python got the LD_LIBRARY_PATH variable just fine, both as a regular user and as root. I

[galaxy-dev] Pulsar on a remote (SGE) cluster

Hi all, We have Pulsar working in a synchronous fashion using RESTful services on our local network. Now, we're trying to use Pulsar on a remote (SGE) cluster and we will not have the ability to mount a shared file system. What is the best way to use Galaxy to queue jobs? If Pulsar is the answe

[galaxy-dev] SGE integration

I'm trying to get my instance of Galaxy working with Sun Grid Engine. The page https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster is not 100% clear on how to do this but I here's what my job_conf.xml looks like:

[galaxy-dev] tool shed updates broken on my local server

Hi there, I am currently trying to migrate our Galaxy production server onto new hardware and I am facing many challenges. Recently I've been unable to update tools from the tool shed. During the migration I've moved across the files, the data, the tools and their dependencies as well as the da

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

Hi Dannon, I tried a few things; /mnt/galaxy/galaxy-app has the universe_wsgi.ini file. I started there. It would be overwritten I then went to the s3 bucket and tried universe_wsgi.ini.cloud. Changed that. It too would eventually be overwritten with the defaults (plus the file above) I c

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

Since there are so many surprising new details in your last mail, maybe it would help if you could tell where you got your Python from. Is it a regular system installation or a toolshed installed version inside Galaxy (which may use its own env.sh to manipulate paths) ? Best, Wolfgang On 29.01

Re: [galaxy-dev] Nothing being tested on Test and main Tool Shed?

On Tue, Jan 27, 2015 at 1:25 PM, Peter Cock wrote: > > On Tue, Jan 27, 2015 at 11:32 AM, Peter Cock > wrote: > > On Wed, Jan 7, 2015 at 2:07 PM, Dave Bouvier wrote: > >> Peter, > >> > >> After fixing a number of issues, it appears that the tests are now running > >> as they should. I'll keep an

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

Ok, a little more progress. This is really strange. It seems that it is only python that is not getting LD_LIBRARY_PATH, and it only doesn't get it if it is being invoked by a user (i.e. not root). If root invokes python then it gets the variable no problem. If the galaxy user invokes it, it does n