Question: bam upload fails because of missing json param fiel
0
gravatar for manuel.pasieka
16 months ago by
manuel.pasieka30 wrote:

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 temp folder.

Any ideas on how this can happen? Thank you!, Manuel

upload • 405 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by manuel.pasieka30

Have you installed SAMtools on your local yet? If not, install and restart then try again. This is a required tool suite when working with BAM/SAM datasets and should be installed on most Galaxy instances.

Let's start troubleshooting there. Thanks, Jen, Galaxy team

ADD REPLYlink written 16 months ago by Jennifer Hillman Jackson25k

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?

thx, Manuel

ADD REPLYlink written 16 months ago by manuel.pasieka30

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 managed above aroused because galaxy depends on a module spelled 'samtools' and we have it installed as 'SAMTools'. I changed the requirement tag in the set_metadata and upload tools xml configuration file to resolve this naming issue.

Can you recommend how to handle such issues in the future? In order to avoid having to edit those config files or rename modules? Is there some kind of module name mapping feature in galaxy? If not, i though about modifying the Module Resolver in order to search for modules in a case insensitive matter and provide the module cmd with the best match of available modules.

thx, Manuel

ADD REPLYlink written 16 months ago by manuel.pasieka30
0
gravatar for manuel.pasieka
16 months ago by
manuel.pasieka30 wrote:

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.

ADD COMMENTlink written 16 months ago by manuel.pasieka30
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