Hi Scott,

Galaxy itself requires samtools (to deal with BAM files), separately
from any Tool Dependency within the tool calling framework.

Right now there is no mechanism for datatype definitions to declare a
dependency (e.g. on a binary like samtools, or a Python library).

Probably samtools should be listed as a requirement on the wiki?
https://wiki.galaxyproject.org/Admin/GetGalaxy

Peter

On Fri, Feb 26, 2016 at 5:49 PM, 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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