On Mon, May 5, 2014 at 3:30 PM, Geert Vandeweyer <geert.vandeweyer2@uantwerpen.be> wrote:
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).
Is samtools on the Galaxy user's $PATH not just your personal account? i.e. Dd you log in as Galaxy to check this? Peter