Hi everyone,
my local installation of Galaxy has an issue with using the "Upload File" tool
on data that was uploaded to the ftp server. The ftp upload itself works fine:
-rwxrwxrwx. 1 65533 65533 4804 2012-08-16 13:52 28S_rRNA.fa
but there seems to be some issue with Galaxy moving it and I have no clue where
the problem is. The final dataset
/galaxy/galaxy_server/database/files/024/dataset_24020.dat is present as a
file, but empty:
-rw-rw-r--. 1 galaxy galaxy 0 2012-08-16 13:53 dataset_24020.dat
I'm grateful for any hints.
Best regards,
Sarah
----- Forwarded Message -----
From: di...@immunbio.mpg.de
To: di...@immunbio.mpg.de, di...@immunbio.mpg.de
Sent: Thursday, August 16, 2012 1:55:04 PM
Subject: Galaxy tool error report from di...@immunbio.mpg.de
GALAXY TOOL ERROR REPORT
------------------------
This error report was sent from the Galaxy instance hosted on the server
"xxx"
-----------------------------------------------------------------------------
This is in reference to dataset id 24020 from history id 1393
-----------------------------------------------------------------------------
You should be able to view the history containing the related history item
115: 28S_rRNA.fa
by logging in as a Galaxy admin user to the Galaxy instance referenced above
and pointing your browser to the following link.
xxx
-----------------------------------------------------------------------------
The user 'di...@immunbio.mpg.de' provided the following information:
-----------------------------------------------------------------------------
job id: 20566
tool id: upload1
-----------------------------------------------------------------------------
job command line:
python /galaxy/galaxy_server/tools/data_source/upload.py /galaxy/galaxy_server
/galaxy/galaxy_server/database/tmp/tmpw_TcHa
/galaxy/galaxy_server/database/tmp/tmpKwHCcx
24020:/galaxy/galaxy_server/database/job_working_directory/020/20566/dataset_24020_files:/galaxy/galaxy_server/database/files/024/dataset_24020.dat
-----------------------------------------------------------------------------
job stderr:
Traceback (most recent call last):
File "/galaxy/galaxy_server/tools/data_source/upload.py", line 403, in
<module>
__main__()
File "/galaxy/galaxy_server/tools/data_source/upload.py", line 392, in
__main__
add_file( dataset, registry, json_file, output_path )
File "/galaxy/galaxy_server/tools/data_source/upload.py", line 289, in
add_file
line_count, converted_path = sniff.convert_newlines( dataset.path,
in_place=in_place )
File "/galaxy/galaxy_server/lib/galaxy/datatypes/sniff.py", line 98, in
convert_newlines
shutil.move( temp_name, fname )
File "/usr/local/lib/python2.7/shutil.py", line 299, in move
copy2(src, real_dst)
File "/usr/local/lib/python2.7/shutil.py", line 129, in copy2
copystat(src, dst)
File "/usr/local/lib/python2.7/shutil.py", line 98, in copystat
os.utime(dst, (st.st_atime, st.st_mtime))
OSError: [Errno 1] Operation not permitted:
'/galaxy/galaxy_server/database/ftp/di...@immunbio.mpg.de/28S_rRNA.fa'
-----------------------------------------------------------------------------
job stdout:
-----------------------------------------------------------------------------
job info:
None
-----------------------------------------------------------------------------
job traceback:
None
-----------------------------------------------------------------------------
(This is an automated message).
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