Unfortunately the ToolShed dependency only provides samtools to individual
Galaxy tools that declare a dependency on it. However, it allows multiple
versions of samtools to be available to different (versions of) Galaxy
tools.

This does NOT provide a samtools on $PATH for Galaxy itself, and it needs
it for uploading and indexing BAM files.

Peter

On Thursday, January 1, 2015, Nathan Kipniss <nkipn...@gmail.com> wrote:

> So I checked, and it is not. (type not found).
> I will try some of the methods suggested on the admin/config wiki. (
> https://wiki.galaxyproject.org/Admin/Config/ToolDependencies)
>
> But something I am confused over is why did the install not go "properly"
> through the toolshed? Or am I missing something in the directions for
> install?
>
>
>
> Best,
> Nathan
>
> On Wed, Dec 31, 2014 at 10:50 AM, Scott Jeschonek <sco...@averesystems.com
> <javascript:_e(%7B%7D,'cvml','sco...@averesystems.com');>> wrote:
>
>> Hi Nathan,
>>
>> is samtools executable in the environment path?
>>
>> Scott
>>
>>
>> On Dec 31, 2014, at 1:49 PM, Nathan Kipniss <nkipn...@gmail.com
>> <javascript:_e(%7B%7D,'cvml','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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>>
>
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