User: manuel.pasieka

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30
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New User
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Last seen:
3 months, 2 weeks ago
Joined:
1 year, 6 months ago
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m*************@vbcf.ac.at

Posts by manuel.pasieka

<prev • 18 results • page 1 of 2 • next >
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nginx missing upload module
... Hello, I am trying to use nginx for handling uploads, and following https://docs.galaxyproject.org/en/master/admin/nginx.html?highlight=nginx i added the galaxy ppa (https://launchpad.net/~galaxyproject/+archive/ubuntu/nginx ) in order to use the precompiled nginx including the upload module. Tryi ...
nginx upload written 3 months ago by manuel.pasieka30
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Comment: C: uWSGI mule setup + nginx fails
... Thank you Nate! This solved the issue, in addition i can reach the web server ok 8080 as well now! ...
written 3 months ago by manuel.pasieka30
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uWSGI mule setup + nginx fails
... Hi, I am trying to setup a new local (none cluster) galaxy installation based on v18.01 that should serve multiple users. Reading the galaxy in production documentation https://docs.galaxyproject.org/en/latest/admin/production.html and https://docs.galaxyproject.org/en/master/admin/scaling.html I ...
socket nginx uwsgi written 3 months ago by manuel.pasieka30 • updated 3 months ago by Nate Coraor3.2k
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Answer: A: Job wrapper fails because of missing file
... Hi, it took me some time (should have read the error message with more attention) **The error happens, as the path on the cluster is not identical as on the machine where galayx is running**. The folder structures on the VM and cluster are different, but I set some soft links in the home directory ...
written 16 months ago by manuel.pasieka30
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Fail to reproduce galaxy job environment
... Hi, I have a Galaxy 16.10 instance submitting onto a PBS controlled cluster using the module system to resolve dependencies. Using the Picard CollectRnaSeqMetrics tool always fails because of the gtfToGenePred that it depends ons. gtfToGenePred: error while loading shared libraries: libpng12.s ...
job environment written 16 months ago by manuel.pasieka30
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Job wrapper fails because of missing file
... Hi, I have difficulties running a picard tool "MarkDuplicates on data" as the Job wrapper script complains about a metadata_temp file to be missing, although the file exits in the job directory and contains data. We using Galaxy v16.10 on a seperate host, submitting to a cluster running PBS Pro, d ...
job wrapper written 16 months ago by manuel.pasieka30
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improve on module name resolving
... Hello, I am using the module dependency resolver to run galaxy task on a cluster, and often have the issue that tools specify their module/tool requirements with a different spelling than the module name on the cluster. e.g. a tool requires samtools, and the module is called SAMtools. I currently ...
module written 17 months ago by manuel.pasieka30
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Comment: C: bam upload fails because of missing json param fiel
... Hello Jennifer, the environment I am running galaxy is a bit of a mess in which the galaxy instance launches its jobs onto a PBSPro managed cluster through a SSH job runner. The galaxy web server and the cluster share the same module system, and i am using the Module Dependency Resolver. The issue m ...
written 17 months ago by manuel.pasieka30
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Answer: A: bam upload fails because of missing json param fiel
... Following Jennifers tip, I found the root of all evil to be the the set_metadata tool that depends on samtools and somehow interfered with the upload script. So making samtools available to both set_metadata and upload solved the issue. ...
written 17 months ago by manuel.pasieka30
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Comment: C: bam upload fails because of missing json param fiel
... Hello Jennifer, I was using a module system to load samtools which might have caused some problems; so I have installed samtools localy on the instance galaxy is running. The launchscript still references a not existing file in the galaxy tmp directory. How should this tmp file be generated? th ...
written 17 months ago by manuel.pasieka30

Latest awards to manuel.pasieka

Scholar 16 months ago, created an answer that has been accepted. For A: Job wrapper fails because of missing file

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