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.
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,NathanOn Wed, Dec 31, 2014 at 10:50 AM, Scott Jeschonek <email@example.com> wrote:Hi Nathan,is samtools executable in the environment path?Scott___________________________________________________________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() 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 directoryWhich 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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