User: manuel.pasieka

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30
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New User
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Last seen:
8 months, 1 week ago
Joined:
10 months, 3 weeks ago
Email:
m*************@vbcf.ac.at

Posts by manuel.pasieka

<prev • 15 results • page 1 of 2 • next >
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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 8 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 8 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 8 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 9 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 9 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 9 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 9 months ago by manuel.pasieka30
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bam upload fails because of missing json param fiel
... Hi, trying to upload a bam file fails on my local galaxy installation as the job script tool_script.sh in the job directory tries to execute galaxy/tools/data_sources.upload.py In the run script, the third argument (whould be the json paramfile) is referencing a none existing file in the galaxy te ...
upload written 9 months ago by manuel.pasieka30
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Keep failed job directory
... Hi, I am very new to galaxy and have to debug some failed job, only that the galaxy.job.output_check??? is removing the job directory of the failed job. Is it possible to disable this cleanup step? I want to check what the job directory contains, and why the job failed. Thx! ...
debug written 10 months ago by manuel.pasieka30 • updated 10 months ago by Devon Ryan1.8k
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Answer: A: Galaxy fails to submit job because of no active DRMAA session
... The problem was caused because of a missing local DRM installation. See this followup [post](https://biostar.usegalaxy.org/p/21354/) ...
written 10 months ago by manuel.pasieka30

Latest awards to manuel.pasieka

Scholar 8 months ago, created an answer that has been accepted. For A: Job wrapper fails because of missing file

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