Question: failed to upload .bam file
gravatar for biowz
3.3 years ago by
United States
biowz0 wrote:
I used samtools merge to merge new bam file. After that, I upload this file, but galaxy can not recognize it. The errors as follow:
Traceback (most recent call last):
  File "/Users/biowzmailustceducn/galaxy/tools/data_source/", line 430, in <module>
  File "/Users/biowzmailustceducn/galaxy/tools/data_source/", line 419, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/Users/biowzmailustceducn/galaxy/tools/data_source/", line 346, in add_file
    if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ):
  File "/Users/biowzmailustceducn/galaxy/lib/galaxy/datatypes/", line 224, in dataset_content_needs_grooming
    version = self._get_samtools_version()
  File "/Users/biowzmailustceducn/galaxy/lib/galaxy/datatypes/", line 187, in _get_samtools_version
    output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/", line 709, in __init__
    errread, errwrite)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/", line 1326, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
bam file • 953 views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson25k • written 3.3 years ago by biowz0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This is a new Galaxy local? Or an existing one? Do other tools work?

To troubleshoot, make sure that you are running the latest build 15.07 and the samtools and picard have been installed from the Tool Shed (with managed dependencies). From a first look, it appears that samtools is missing (required).

Thanks and let us know how this goes, Jen, Galaxy team

ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k

Hi Jen, I am not sure whether it is new or old one.How I can check the version of galaxy? I did not install samtools or picard independently, only as appliance tool for Tophat2. How I update my local galaxy? Thank you very much for your great help. Best wishes   Hill





ADD REPLYlink written 3.3 years ago by biowz0
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