Problem with executing newly installed tools (via admin)

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

Problem with executing newly installed tools (via admin)

Nicolas Cybulski

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'', u''])

The problem seems to be a duplicate entry of the tool_id

[u'', u'']

In the shed_tool_conf.xml the tools are generated as follows

<tool file="" guid="">

If I change this guid to something less complicated like

<tool file="" 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,


Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

To search Galaxy mailing lists use the unified search at: