So I checked, and it is not. (type not found).
I will try some of the methods suggested on the admin/config wiki. (

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?


On Wed, Dec 31, 2014 at 10:50 AM, Scott Jeschonek <> wrote:
Hi Nathan,

is samtools executable in the environment path?  


On Dec 31, 2014, at 1:49 PM, Nathan Kipniss <> 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/", line 407, in <module>
  File "/home/galaxy/galaxy-dist/tools/data_source/", line 396, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/home/galaxy/galaxy-dist/tools/data_source/", 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/", line 147, in dataset_content_needs_grooming
    version = self._get_samtools_version()
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/", line 129, in _get_samtools_version
    output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]
  File "/usr/lib/python2.7/", line 710, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/", 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?
Nathan Kipniss

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