Re: [galaxy-dev] Singularity Container forks ?

Hi, It's seems like you got me ! yey ! :D I was already working on my fork for singularity , since we don't need any sudo rights for the galaxy user "setup manually by the admin and the paths hard-coded for each tool " I will test it out and let you know ! Best regards from Greece, Nikos

[galaxy-dev] Galaxy slurm error

Has anyone ever encountered an error such as this when running galaxy with slurm and submitting files for upload and unzip. slurmstepd: get_exit_code task 0 died by signal ___ Please keep all replies on the list by using "reply all" in

[galaxy-dev] drmaa job status

Dear list, I have two question for all DRMAA users. Here is the first one. I was checking how our queuing system (univa GridEngine) and Galaxy react if jobs are submitted that exceed run time or memory limits. I found out that the python drmaa library cannot query the job status after the

[galaxy-dev] drmaa resubmission

Dear list, I was thinking about implementing the job resubmission feature for drmaa. I hope that I can simplify the job configuration for our installation (and probably others as well) by escalating through different queues (or ressource limits). Thereby I hope to reduce the number of special

Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hi Same for me. But It looks like to be related with tools installed via the toolshed (Ie : bedtools, emboss, blast+ suite...). My own tools seem to be ok. Just like you Edgar, nothing in the log... Fred De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De la part de

Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hello Frederic, I actually just fixed the problem not 5 minutes ago... In your file: /etc/httpd/vhosts.d/galaxy_prod.conf Add the following line: AllowEncodedSlashes NoDecode Please let me know what you think... Regards, Edgar Fernandez System Administrator (Linux) Technologies de

Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hi Edgar, Frederic, if you are using Apache as proxy for your Galaxy server, then you should probably add |AllowEncodedSlashes NoDecode| to your Apache config, see https://galaxyproject.org/admin/config/apache-proxy/#allow-encoded-slashes-in-urls Cheers, Nicola On 15/06/17 15:35, SAPET,

Re: [galaxy-dev] drmaa job status

Matthias, We have had this problem on our SGE based installation for years. We referred to it as the "green screen of death" - as it would allow a biologist to continue analysis using output that was partial, at best, often resulting in seemingly successful completion of the entire analysis,

Re: [galaxy-dev] Galaxy slurm error

I would guess something about the slurm job exceeded some allocated resource (memory, cpu, time) and slurm killed the job. David Hoover HPC @ NIH > On Jun 15, 2017, at 11:28 AM, Nate Coraor wrote: > > Hi Evan, > > Are there any other details logged for this job? > > --nate

Re: [galaxy-dev] Galaxy slurm error

If slurm accounting is configured, `sacct` might reveal more. You might also check the slurmd logs on the execution host where the job ran. --nate On Thu, Jun 15, 2017 at 11:47 AM, Hoover , David (NIH/CIT) [E] < hoove...@helix.nih.gov> wrote: > I would guess something about the slurm job

Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hello, Nice ! Thank you for the help. Regards, Fred De : Fernandez Edgar [mailto:edgar.fernan...@umontreal.ca] Envoyé : jeudi 15 juin 2017 16:41 À : SAPET, Frederic ; galaxy-...@bx.psu.edu Objet : RE: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hello, Thank you as well, Is that a new behavior with 17.05 ? I use the Apache proxy since a while without any problem, with previous versions of Galaxy. Regards, Fred De : Nicola Soranzo [mailto:nicola.sora...@gmail.com] De la part de Nicola Soranzo Envoyé : jeudi 15 juin 2017 16:44 À :

Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

According to the same documentation, you need it only if using the |mod_proxy| Apache module with HTTP transport, but I'm using nginx, not Apache, so I'm not the best person to ask. Cheers, Nicola On 15/06/17 15:55, Fernandez Edgar wrote: Thanks Nicola for the comfirmation. Would you mind

Re: [galaxy-dev] drmaa job status

Hi Matthias, I can't speak for GridEngine's specific behavior because I haven't used it in a long time, but it's not surprising that jobs "disappear" as soon as they've exited. Unfortunately, Galaxy uses periodic polling rather than waiting on completion. We'd need to create a

Re: [galaxy-dev] Galaxy slurm error

Hi Evan, Are there any other details logged for this job? --nate On Thu, Jun 15, 2017 at 9:20 AM, evan clark wrote: > Has anyone ever encountered an error such as this when running galaxy with > slurm and submitting files for upload and unzip. > > slurmstepd: get_exit_code

Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hi Fred, It was already needed for data manager tools in 17.01, it seems it's needed for all tools installed from the ToolShed since 17.05, but I use nginx, not Apache. Cheers, Nicola On 15/06/17 15:57, SAPET, Frederic wrote: Hello, Thank you as well, Is that a new behavior with 17.05 ?