On Dec 21, 2011, at 3:48 AM, Makis Ladoukakis wrote:

> Seems like an error concerning permissions in your galaxy folders. Try:
> 
> sudo chmod 777 galaxy-dist/
> 
> and then try to upload data again.

Setting world-writable should be considered a last resort in any scenario.  The 
problem here seems to be that samtools can't be executed.  Is it installed on 
whatever system is executing the upload tool?

--nate

> 
> To: galaxy-...@bx.psu.edu
> From: liisa.ko...@dnalandmarks.ca
> Date: Tue, 20 Dec 2011 16:22:02 -0500
> Subject: [galaxy-dev] Problem uploading files from filesystem paths
> 
> Hi, 
> I'm trying to upload data to Data Libraries from filesystems paths as Admin. 
> I get the following error. 
> Any ideas? 
> 
> Thanks in advance, 
> Liisa 
> 
> 
> Traceback (most recent call last): File 
> "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 394, in 
> __main__() File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 
> 386, in __main__ add_file( dataset, registry, js 
> Job Standard Error 
> Traceback (most recent call last):
>  File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 394, in 
>    __main__()
>  File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 386, in 
> __main__
>    add_file( dataset, registry, json_file, output_path )
>  File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 300, in 
> add_file
>    if datatype.dataset_content_needs_grooming( dataset.path ):
>  File "/data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in 
> dataset_content_needs_grooming
>    version = self._get_samtools_version()
>  File "/data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in 
> _get_samtools_version
>    output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, 
> stdout=subprocess.PIPE ).communicate()[1]
>  File "/usr/lib64/python2.6/subprocess.py", line 633, in __init__
>    errread, errwrite)
>  File "/usr/lib64/python2.6/subprocess.py", line 1139, in _execute_child
>    raise child_exception
> OSError: [Errno 13] Permission denied
> 
> 
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