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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi,<br>
<br>
I have followed the advice given in <a href="http://environmentalomics.org/bio-linux-galaxy/" target="_blank">
http://environmentalomics.org/bio-linux-galaxy/</a> and I have successfully set up the galaxy-server-apache-proxy. I have put a sam file (ex1.sam) in the transfer directory for manager@localhost and can see the file in the'Files uploaded via FTP' section.
However, when I try to select and upload the file I get errors:<br>
<br>
<b>From the debug message:</b><br>
Traceback (most recent call last):<br>
File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 394, in <module><br>
__main__()<br>
File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 383, in __main__<br>
add_file( dataset, registry, json_file, output_path )<br>
File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 278, in add_file<br>
line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place )<br>
File "/usr/lib/galaxy-server/lib/galaxy/datatypes/sniff.py", line 116, in convert_newlines<br>
shutil.move( temp_name, fname )<br>
File "/usr/lib/python2.7/shutil.py", line 302, in move<br>
copy2(src, real_dst)<br>
File "/usr/lib/python2.7/shutil.py", line 130, in copy2<br>
copyfile(src, dst)<br>
File "/usr/lib/python2.7/shutil.py", line 83, in copyfile<br>
with open(dst, 'wb') as fdst:<br>
IOError: [Errno 13] Permission denied: u'/var/lib/galaxy-server/transfer/manager@localhost/ex1.sam'<br>
<br>
<br>
<b>From the server.log:</b><br>
galaxy.tools.actions.upload_common INFO 2015-01-16 10:35:07,359 tool upload1 created job id 2<br>
127.0.0.1 - - [16/Jan/2015:10:35:07 +0000] "POST /galaxy/tool_runner/index HTTP/1.1" 200 - "http://localhost/galaxy/tool_runner?tool_id=upload1" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0"<br>
galaxy.jobs DEBUG 2015-01-16 10:35:07,485 (2) Working directory for job is: /usr/lib/galaxy-server/database/job_working_directory/000/2<br>
galaxy.jobs.handler DEBUG 2015-01-16 10:35:07,496 (2) Dispatching to local runner<br>
127.0.0.1 - - [16/Jan/2015:10:35:07 +0000] "GET /galaxy/api/histories/1cd8e2f6b131e891/contents HTTP/1.1" 200 - "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0"<br>
galaxy.jobs DEBUG 2015-01-16 10:35:07,599 (2) Persisting job destination (destination id: local:///)<br>
galaxy.jobs.handler INFO 2015-01-16 10:35:07,622 (2) Job dispatched<br>
galaxy.tools.deps DEBUG 2015-01-16 10:35:07,770 Building dependency shell command for dependency 'samtools'<br>
galaxy.tools.deps WARNING 2015-01-16 10:35:07,770 Failed to resolve dependency on 'samtools', ignoring<br>
galaxy.jobs.runners DEBUG 2015-01-16 10:35:07,833 (2) command is: python /usr/lib/galaxy-server/tools/data_source/upload.py /usr/lib/galaxy-server /usr/lib/galaxy-server/database/tmp/tmp7LWfBs /usr/lib/galaxy-server/database/tmp/tmp9nLfry 2:/usr/lib/galaxy-server/database/job_working_directory/000/2/dataset_2_files:/usr/lib/galaxy-server/database/files/000/dataset_2.dat<br>
galaxy.jobs.runners.local DEBUG 2015-01-16 10:35:07,834 (2) executing job script: /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy_2.sh<br>
galaxy.jobs DEBUG 2015-01-16 10:35:07,862 (2) Persisting job destination (destination id: local:///)<br>
galaxy.jobs.runners.local DEBUG 2015-01-16 10:35:08,617 execution finished: /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy_2.sh<br>
galaxy.tools.deps DEBUG 2015-01-16 10:35:08,684 Building dependency shell command for dependency 'samtools'<br>
galaxy.tools.deps WARNING 2015-01-16 10:35:08,684 Failed to resolve dependency on 'samtools', ignoring<br>
galaxy.jobs.runners DEBUG 2015-01-16 10:35:08,684 executing external set_meta script for job 2: /usr/lib/galaxy-server/set_metadata.sh ./database/files /usr/lib/galaxy-server/database/job_working_directory/000/2 . /tmp/universe_wsgi_jymQ.ini /usr/lib/galaxy-server/database/tmp/tmp7LWfBs
/usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy.json /usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_eqLSN4,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_Y8KWCA,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_e8sRbx,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_s439LW,,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_jlOhII<br>
galaxy.jobs.runners DEBUG 2015-01-16 10:35:09,731 execution of external set_meta for job 2 finished<br>
galaxy.jobs DEBUG 2015-01-16 10:35:09,789 setting dataset state to ERROR<br>
galaxy.jobs DEBUG 2015-01-16 10:35:09,874 job 2 ended<br>
galaxy.datatypes.metadata DEBUG 2015-01-16 10:35:09,874 Cleaning up external metadata files<br>
127.0.0.1 - - [16/Jan/2015:10:35:11 +0000] "GET /galaxy/api/histories/1cd8e2f6b131e891/contents HTTP/1.1" 200 - "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0"<br>
127.0.0.1 - - [16/Jan/2015:10:35:11 +0000] "GET /galaxy/api/histories/1cd8e2f6b131e891 HTTP/1.1" 200 - "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0"<br>
<br>
<br>
I noticed permission being mentioned. The status of the transfer directory is:<br>
drwxr-xr-x 2 root root 4096 Jan 16 10:12 manager@localhost<br>
<br>
I change this to:<br>
drwxr-xr-x 2 manager manager 4096 Jan 16 10:12 manager@localhost<br>
<br>
But the same thing happened.<br>
<br>
Has anyone seen this problem before and have and guidance?<br>
<br>
Thank you,<br>
Ian<br>
<br>
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