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.szakony...@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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