Question: Local Tophat Error "OSError: [Errno 2] No such file or directory"
0
gravatar for jmnm2201
2.2 years ago by
jmnm22010
South Africa
jmnm22010 wrote:

Hi All!

I have recently migrated to using a new local instance of galaxy at my university. I am having problems executing tophat.  I have pasted the error below.  Can anyone give me a hint on what the problem might be? Funny thing is that the output files are generated and contains some content, but Tophat is unable to complete the job.

 

"The Galaxy framework encountered the following error while attempting to run the tool:

Traceback (most recent call last):
  File "/opt/exp_soft/galaxy/srvubugal002/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/opt/exp_soft/galaxy/srvubugal002/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1124, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )  # call datatype.set_meta directly for the initial set_meta call during dataset creation
  File "/opt/exp_soft/galaxy/srvubugal002/galaxy-dist/lib/galaxy/datatypes/binary.py", line 244, in set_meta
    proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
  File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory"

 

Thanks

 

JM

error tophat admin local samtools • 1.0k views
ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson23k • written 2.2 years ago by jmnm22010
1
gravatar for Daniel Blankenberg
13 months ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:

You should be able to define a "default" samtools under your tool dependency directory that will be pick-upped by the set metadata process. See e.g. https://wiki.galaxyproject.org/Admin/Config/ToolDependencies

ADD COMMENTlink written 13 months ago by Daniel Blankenberg ♦♦ 1.7k
1
gravatar for Bjoern Gruening
2.2 years ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k wrote:
Hi, you need to have samtools on your PATH to generate metadata for BAM files, like the index or to sort the file. Hope this helps, Bjoern
ADD COMMENTlink written 2.2 years ago by Bjoern Gruening4.8k
0
gravatar for Bjoern Gruening
2.2 years ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k wrote:
Hi, you need to have samtools on your PATH to generate metadata for BAM files, like the index or to sort the file. Hope this helps, Bjoern
ADD COMMENTlink written 2.2 years ago by Bjoern Gruening4.8k
0
gravatar for jmnm2201
2.2 years ago by
jmnm22010
South Africa
jmnm22010 wrote:

Thank you! Will follow up with our galaxy admin.

ADD COMMENTlink written 2.2 years ago by jmnm22010
0
gravatar for deane
13 months ago by
deane30
deane30 wrote:

This issue should be fixed by the tophat tool maintainer. All other tools that I have used put the proper path in the tool definition. For some reason Tophat (even old versions) need the path in the environment of the galaxy server. I spent over a week trying to find the cause of the error. The problem with putting it in your path is that if you install another version of tophat you'll have to put a path to that version also.

Jen, I hope you will refer this to the tophat developers.

Thanks, Deane

ADD COMMENTlink written 13 months ago by deane30

Passed on and under discussion. Recent Conda changes impact how to resolve this.

And so you and others know, it is not really Tophat that is missing Samtools, it is an underlying process. Galaxy requires Samtools to fully function even without any other installed tools (just at default). It should probably be the first tool set up on any instance. We do not distribute Samtools with Galaxy since it may update between Galaxy releases, some tools have specific version dependencies, and the like.

This critical need for Samtools could be better communicated/documented. That is part of the end goal when resolving this.

ADD REPLYlink written 13 months ago by Jennifer Hillman Jackson23k
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