On Mon, May 5, 2014 at 3:30 PM, Geert Vandeweyer
<geert.vandewey...@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
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