Question: Problem uploading BAM file
0
gravatar for stephane.roche
4.2 years ago by
France
stephane.roche10 wrote:

I have a problem after uploading a BAM file. This file have the state ERROR in my local installation of Galaxy whereas in a public distribution, it have not. I am working with an Xubuntu. Pyhthon 2.7.6 is installed. I suspect an problem with python interpreter.

Could you help me ?

 

Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 407, in <module>
    __main__()
  File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 396, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 324, in add_file
    if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ):
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 145, in dataset_content_needs_grooming
    version = self._get_samtools_version()
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 127, in _get_samtools_version
    output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]
  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

 

software error • 1.7k views
ADD COMMENTlink modified 4.1 years ago • written 4.2 years ago by stephane.roche10
0
gravatar for Jennifer Hillman Jackson
4.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi,

Is Samtools installed and in the Galaxy user's path? This is usually the issue when BAM files fail to upload. You can install it from the Tool Shed - grab the most current version. Then try to execute a command line-command on the file, maybe bam to sam, to confirm it is working.

Best, Jen, Galaxy team

ADD COMMENTlink written 4.2 years ago by Jennifer Hillman Jackson25k
0
gravatar for stephane.roche
4.1 years ago by
France
stephane.roche10 wrote:

I have a problem with samtools dependencie. I have a WARNING message of samtools dependencies at the end of the upload of a BAM file. the message is :

galaxy.tools.deps WARNING 2014-10-08 16:05:53,746 Failed to resolve dependency on 'samtools', ignoring
galaxy.tools.deps WARNING 2014-10-08 16:05:55,090 Failed to resolve dependency on 'samtools', ignoring

 

The main problem is that I have no message in shed_tools manager and in the "terminal" trace of galaxy about a problem of dependency. Even with a update.

The others application using samtools works correctly.

Best Regards

Stephane

 

ADD COMMENTlink written 4.1 years ago by stephane.roche10
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