Hi,
I have installed the Picard tools using the Tool-shed functionality in
the admin tools.
The tools and requisites have been correctly installed and run correctly.
The insert statement to the event table fails however. I get the
following error on screen:
|OperationalError: (OperationalError) (1241, 'Operand should contain 1
column(s)') 'INSERT INTO event (create_time, update_time, history_id,
user_id, message, session_id, tool_id) VALUES (%s, %s, %s, %s, %s, %s,
%s)' (datetime.datetime(2014, 4, 2, 9, 32, 47, 823142),
datetime.datetime(2014, 4, 2, 9, 32, 47, 823170), 35L, 4L, "Tool params:
{'histWidth': u'0', 'deviations': u'10.0', 'malevel': u'ALL_READS',
'input_file': u'5266', 'out_prefix': u'Insertion size metrics',
'refresh': u'refresh', 'minPct': u'0.05', 'tool_state':
u'800254cf010000316164663833323133363237333739303833323639353065346362343762393730383966363664313a37623232363836393733373435373639363437343638323233613230323235633232333035633232323232633230323236343635373636393631373436393666366537333232336132303232356332323331333032653330356332323232326332303232363936653730373537343566363636393663363532323361323032323335333233363336323232633230323235663566373036313637363535663566323233613230333032633230323235663566373236353732373536653566373236353664363137303566366136663632356636393634356635663232336132303665373536633663326332303232366436313663363537363635366332323361323032323563323234313463346335663532343534313434353335633232323232633230323236663735373435663730373236353636363937383232336132303232356332323439366537333635373237343639366636653230373336393761363532303664363537343",
1468L,
[u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0',
u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0'])
|The problem seems to be a duplicate entry of the tool_id
|[u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0',
u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0']
|In the shed_tool_conf.xml the tools are generated as follows
<tool
file="toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardInsertSize.xml"
guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0">
If I change this guid to something less complicated like
<tool
file="toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardInsertSize.xml"
guid="testPicard">
and restart galaxy it works ...
for all tools (so not only the one that I've changed).
Does anyone have an idea as to why this is ?
kind regards,
Nicolas
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