I too had trouble with BAM files as

Line 201
class Bam( Binary ):
    def _get_samtools_version( self ):
        samtools_exec = which('samtools')

Assumes samtools is installed on the server and was not fining one.

I had to install samtools outside of galaxy to get past that.

University of Manchester
From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Scott Szakonyi [scott.b.szakony...@nd.edu]
Sent: Friday, February 26, 2016 5:49 PM
To: Galaxy Dev Mailing List
Subject: [galaxy-dev] Difficulty uploading BAM files


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<http://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>
  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 

Best regards,

Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556
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