Hi,

I'm having trouble uploading BAM files in our development environment. Other files types are uploading without issue. I'm testing with a small BAM file I downloaded, and I'm able to successfully upload it on our production server and usegalaxy.org. When I try to upload in the development environment, I get the following error:

Traceback (most recent call last):

  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 431, in <module>

    __main__()

  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 420, in __main__

    add_file( dataset, registry, json_file, output_path )

  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 347, in add_file

    if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ):

  File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 218, in dataset_content_needs_grooming

    version = self._get_samtools_version()

  File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 179, in _get_samtools_version

    raise Exception(message)

Exception: Attempting to use functionality requiring samtools, but it cannot be located on Galaxy's PATH.

I've checked my installed tools, and all the same Samtools packages are successfully installed on the development environment as in production. I don't see any missing dependencies or anything like that. At this point I'm stumped. If anyone can offer some guidance on how to resolve this, I'd be most appreciative.

Best regards,

--

Scott B. Szakonyi

Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu

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