November 2016 - galaxy-dev - lists.galaxyproject.org

Galaxy+Slurm (with elastic cluster) error: "Job output not returned from cluster"
by Marco Tangaro 02 Nov '16

02 Nov '16

Dear all, I've a issue using Galaxy with elastic cluster support. It is provided by integrating SLURM and a worker node is added as soon as jobs are submitted through the Galaxy portal. When a job is submitted, the node takes some minutes to be configured. After ~7 minutes, Galaxy give me a failure message "Job output not returned from cluster". On the contrary if the node is already up, everything is ok. I tried only a very simple job getting the UCSC human genome. I'm using the master galaxy branch with postgresq+nginx+uwsgi+proftpd. Here is my job_conf.xml configuration: https://gist.github.com/mtangaro/c0528c3d9a7b44b3bab35dbd947f2c81 I'm not a slurm expert. I went through the mailing list archive, but I did not solved the issue. Thanks a lot for your help. Marco

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IEs and fancy visualisations
by Björn Grüning 02 Nov '16

02 Nov '16

This is for all Interactive Environment fans that like awesome visualisations! Our friends from IOBIO have created a blog post about an fantastic collaboration between IOBIO and Galaxy: http://iobio.io/2016/11/02/galaxy-integration/ Thanks Chase and Yi - great work! Bjoern

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Compiling dependencies in galaxy yields error
by evan clark 01 Nov '16

01 Nov '16

I was installing a tool from the galaxy toolshed and one of the dependencies was missing due to a bad link. I modified the install files to use the same version of the the software except from a local directory, however galaxy renders a large error when compiling. If I compile the source in the same location outside of galaxy it compiles and installs correctly. The specific package I am attempting to install is ghostscript for homer package.

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