Re: [galaxy-dev] Rocks cluster; jobs run but Galaxy can't find jobid when submitted via drmaa

I forgot to point out the needs of sharing folders and checking the UID/GID of the galaxy user between your systems (and his access to SGE). Remy 2016-01-20 16:00 GMT+01:00 Rémy Dernat : > Hi Eric, > > Here we use both solutions: Galaxy and RocksCluster. In Galaxy, you have >

Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

On Wed, Jan 20, 2016 at 2:43 PM, Gildas Le Corguillé wrote: > Hi, > > A long time ago, in a far far svn repo, we did this "multiple=true" on Peter > wrappers. > > I will try to propose it quickly :) > > Gildas Great - a pull request against

[galaxy-dev] Data Collection collection_type list:list

Hi, I was wondering if creating data collection of collection_type="list:list" is possible? Because I can see only list, pair and list of pairs options available. Why I am asking this question is because I saw this snippet from cuffdiff tool which includes collection_type="list:list" as below.

Re: [galaxy-dev] Data Collection collection_type list:list

list:list (as well as list:list:paired, list:list:list, etc...) can be created via the API or using tools. As an example of the second - if you had a tool that took in a dataset and split it into a list and then mapped a list over that tool - Galaxy would produce a list:list output from the

Re: [galaxy-dev] Rocks cluster; jobs run but Galaxy can't find jobid when submitted via drmaa

Thanks, Remy. I went through the cluster documentation and our Rocks environment seems to be configured properly, after all. It appears that my issue may be related to the UCSC Main table browser. The jobs that Galaxy reports have failed are leaving the job_working_directory behind, with

Re: [galaxy-dev] Running Galaxy jobs remotely via ssh / rsh

Even if you just have two servers, I would strongly recommend you setup a cluster distributed resource manager (DRM) like SLURM, PBS, or Condor and ensuring there exists a shared file system between Galaxy and the node running the jobs. You wouldn't even need to use the CLI job runner - you could

Re: [galaxy-dev] Sample tracking / external services - still supported?

Hi Matthias: I think it’s abandoned, I’ve tried to use it with no success. I think it should be brought up to date or be removed to save people from wasting time trying to get it working. Brad -- Brad Langhorst, Ph.D. Development Scientist New England Biolabs > On Jan 20, 2016, at 3:06 AM,

Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

On Wed, Jan 20, 2016 at 9:19 AM, Floreline TOUCHARD wrote: > Hi, > > I would like to add some tools of the EMBOSS suite (6.6.0) to my Galaxy > instance. It seems that the only wrapper available for Galaxy is for the > 5.0.0 version >

[galaxy-dev] Ansible roles: galaxy_server_dir vs galaxy_home_dir and galaxy_root

Hi there We've just finished provisioning a new Galaxy server here using the ansible-galaxy and ansible-galaxy-extras roles, with some extra roles from Nate and our own creation. In the ansible-galaxy role Galaxy's install location is set using the galaxy_server_dir variable, but in

[galaxy-dev] Galaxy sending jobs to multiple clusters

Hi, John, Dan, Carrie and all others, I am considering a task of setting up a Galaxy instance which shall send jobs to more than on cluster at a time. In my case I am using drmaa-python and I was wondering if it was possible to configure multiple drmaa runners each "pointing" at a different

[galaxy-dev] RedHat versus CentOs

Dear All Our production Galaxy server has been running smoothly on a single multicore box with Red Hat 6.7. As this box gets older and older, it is in now time to replace it. At the same time, we are also considering switching the operating system to CentOS 7. Has anyone switched a

Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

On Wed, Jan 20, 2016 at 2:22 PM, Floreline TOUCHARD wrote: > Thanks for the answer ! > > I compared the two versions of tools. It does not seem to be any major > differences indeed. I added these tools to my instance successfully. Great :) > Additional options in

Re: [galaxy-dev] Sample tracking / external services - still supported?

Hello Matthias, As you correctly identified the original implementation, in spite of being present in the Galaxy distribution, is treated as deprecated. However I know about three sample tracking implementation based on Galaxy's old sample tracking. - *TRON Mainz*

Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

Hi, A long time ago, in a far far svn repo, we did this "multiple=true" on Peter wrappers. I will try to propose it quickly :) Gildas - Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateforme ABiMS (Analyses and

Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

Thanks for the answer ! I compared the two versions of tools. It does not seem to be any major differences indeed. I added these tools to my instance successfully. Additional options in version 6 are not to be integrate to my Galaxy instance immediately. I will update my XML file later if need