Hi,

I'm having issues uploading bam files to our galaxy server. It fails for both FTP and browser upload. Upload.py is executed on the local job runner.

The error is:

Traceback (most recent call last): File "/galaxy/galaxy-dist/tools/data_source/upload.py", line 390, in <module> __main__() File "/galaxy/galaxy-dist/tools/data_source/upload.py", line 379, in __main__ add_file( dataset, registry, json_file, output_path ) File "/galaxy/galaxy-dist/tools/data_source/upload.py", line 318, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 144, in dataset_content_needs_grooming version = self._get_samtools_version() File "/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 128, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib/python2.6/subprocess.py", line 633, in __init__ errread, errwrite) File "/usr/lib/python2.6/subprocess.py", line 1139, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

The logs show 'galaxy.tools.deps WARNING 2014-05-05 15:39:20,676 Failed to resolve dependency on 'samtools', ignoring'

I do have samtools in my path (~/bin/samtools).

Also, the file is actually uploaded fine (can be downloaded again correctly), but cannot be used in galaxy due to its 'error' state.

Any advice on how to solve this?

Best,

Geert