Hello Scott,

you do need a samtools binary on GALAXY's PATH.
This is not samtools installed from the toolshed.

Best,
Marius

On 26 February 2016 at 18:49, Scott Szakonyi <Scott.B.Szakonyi.1@nd.edu> wrote:
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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