[Bio-Linux] Problem with adding data to GALAXY using FTP upload via transfer directory

[Ian Donaldson]

Hi,

I have followed the advice given in http://environmentalomics.org/bio-linux-galaxy/ 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 at 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:

>From the debug message:
Traceback (most recent call last):
  File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 394, in <module>
    __main__()
  File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 383, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 278, in add_file
    line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place )
  File "/usr/lib/galaxy-server/lib/galaxy/datatypes/sniff.py", line 116, in convert_newlines
    shutil.move( temp_name, fname )
  File "/usr/lib/python2.7/shutil.py", line 302, in move
    copy2(src, real_dst)
  File "/usr/lib/python2.7/shutil.py", line 130, in copy2
    copyfile(src, dst)
  File "/usr/lib/python2.7/shutil.py", line 83, in copyfile
    with open(dst, 'wb') as fdst:
IOError: [Errno 13] Permission denied: u'/var/lib/galaxy-server/transfer/manager at localhost/ex1.sam'


>From the server.log:
galaxy.tools.actions.upload_common INFO 2015-01-16 10:35:07,359 tool upload1 created job id 2
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"
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
galaxy.jobs.handler DEBUG 2015-01-16 10:35:07,496 (2) Dispatching to local runner
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"
galaxy.jobs DEBUG 2015-01-16 10:35:07,599 (2) Persisting job destination (destination id: local:///)
galaxy.jobs.handler INFO 2015-01-16 10:35:07,622 (2) Job dispatched
galaxy.tools.deps DEBUG 2015-01-16 10:35:07,770 Building dependency shell command for dependency 'samtools'
galaxy.tools.deps WARNING 2015-01-16 10:35:07,770 Failed to resolve dependency on 'samtools', ignoring
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
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
galaxy.jobs DEBUG 2015-01-16 10:35:07,862 (2) Persisting job destination (destination id: local:///)
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
galaxy.tools.deps DEBUG 2015-01-16 10:35:08,684 Building dependency shell command for dependency 'samtools'
galaxy.tools.deps WARNING 2015-01-16 10:35:08,684 Failed to resolve dependency on 'samtools', ignoring
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
galaxy.jobs.runners DEBUG 2015-01-16 10:35:09,731 execution of external set_meta for job 2 finished
galaxy.jobs DEBUG 2015-01-16 10:35:09,789 setting dataset state to ERROR
galaxy.jobs DEBUG 2015-01-16 10:35:09,874 job 2 ended
galaxy.datatypes.metadata DEBUG 2015-01-16 10:35:09,874 Cleaning up external metadata files
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"
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"


I noticed permission being mentioned.  The status of the transfer directory is:
drwxr-xr-x 2 root root 4096 Jan 16 10:12 manager at localhost

I change this to:
drwxr-xr-x 2 manager manager 4096 Jan 16 10:12 manager at localhost

But the same thing happened.

Has anyone seen this problem before and have and guidance?

Thank you,
Ian

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