failed to upload .bam file

Question: failed to upload .bam file

3.3 years ago by

biowz • 0

United States

biowz • 0 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/upload.py", line 430, in <module>
    __main__()
  File "/Users/biowzmailustceducn/galaxy/tools/data_source/upload.py", line 419, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/Users/biowzmailustceducn/galaxy/tools/data_source/upload.py", 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/binary.py", line 224, in dataset_content_needs_grooming
    version = self._get_samtools_version()
  File "/Users/biowzmailustceducn/galaxy/lib/galaxy/datatypes/binary.py", 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/subprocess.py", line 709, in __init__
    errread, errwrite)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1326, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

bam file • 953 views

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modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.3 years ago by biowz • 0

3.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 3.3 years ago by biowz • 0

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