Hi Christopher,

If your galaxy is configured to set metadata externally then you shouldn't see samtools index being run on the node that runs galaxy (On a side-note galaxy will use pysam starting from release 18.01). One possibility is that the metadata setting failed, and it has been tried again internally. You can control this with the `retry_metadata_internally` option in your galaxy.yml / galaxy.ini file.

Best, Marius

On 24 April 2018 at 15:55, Previti christopher.previti@dkfz-heidelberg.de wrote:

Dear all,

We found something strange with our Galaxy instance...

Our Galaxy server is configured as a submit node using slurm to submit to our cluster.

This works fine for the most part, but today we saw a samtools index job running "locally" on the submit node instead of a cluster node.

Is there any way of stopping this behavior? The submit nodes are not configured for data-intensive computation and everything runs significantly slower.

I was running bamtools (splitting a bam-file into mapped into unmapped) at the time and the output bam-files were being indexed.

Thanks and best regards,

Christopher

*Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician

German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661

christopher.previti@dkfz.de http://www.dkfz.de/ www.dkfz.de

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