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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to