Question: Problem uploading BAM file
gravatar for stephane.roche
4.2 years ago by
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/", line 407, in <module>
  File "/home/galaxy/galaxy-dist/tools/data_source/", line 396, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/home/galaxy/galaxy-dist/tools/data_source/", 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/", line 145, in dataset_content_needs_grooming
    version = self._get_samtools_version()
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/", line 127, in _get_samtools_version
    output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]
  File "/usr/lib/python2.7/", line 710, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/", 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
gravatar for Jennifer Hillman Jackson
4.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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
gravatar for stephane.roche
4.1 years ago by
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 : WARNING 2014-10-08 16:05:53,746 Failed to resolve dependency on 'samtools', ignoring 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



ADD COMMENTlink written 4.1 years ago by stephane.roche10
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