Hi Nathan,

is samtools executable in the environment path?  

Scott


> On Dec 31, 2014, at 1:49 PM, Nathan Kipniss <nkipn...@gmail.com> wrote:
> 
> Hi All,
> 
> New to galaxy here. I'm having an issue uploading bam files into a local 
> instance of galaxy. I understand that it requires samtools, and I installed 
> the appropriate dependency from the toolshed. However, I get the following 
> error:
> 
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 407, in 
> <module>
>     __main__()
>   File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 396, in 
> __main__
>     add_file( dataset, registry, json_file, output_path )
>   File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 324, in 
> add_file
>     if link_data_only == 'copy_files' and 
> datatype.dataset_content_needs_grooming( output_path ):
>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 147, 
> in dataset_content_needs_grooming
>     version = self._get_samtools_version()
>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 129, 
> in _get_samtools_version
>     output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, 
> stdout=subprocess.PIPE ).communicate()[1]
>   File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
>     errread, errwrite)
>   File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
>     raise child_exception
> OSError: [Errno 2] No such file or directory
> 
> Which leads me to believe something is wrong with the install (can't find 
> samtools). The dependency directory is also set. Is there another step I'm 
> missing, or is it better to not install dependencies via the toolshed?
> Best,
> Nathan Kipniss
> 
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