Please keep all replies on the list by using "reply all" I am not really a tool shed expert, hence I can only direct you to the wiki pages: http://wiki.galaxyproject.org/Tool%20Shed Hans-Rudolf On 08/20/2013 12:12 PM, Richard Kuo wrote:

Hello Hans-Rudolf,

I am wondering if the issue could have been caused by the tool shed? I had been playing around with adding new tools via the tool shed just before this happened. The sys admin has restored our Galaxy instance to a previous time point before I did all this and it seems to be working alright now. Is there any documentation of how the tool shed interacts with the conf files within the galaxy folder?

Thank you! Richard

On Mon, Aug 19, 2013 at 12:32 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:

Hi Richard

this looks like a system error to me (and has nothing to do with the galaxy server itself). Something is wrong with your disk? which might also be the original reason why you got complaints about the upload speed.

Sorry, I can't help you any further. I suggest you contact your sys admin.

Regards, Hans-Rudolf

On 08/19/2013 01:07 PM, Richard Kuo wrote:

Hello,

I tried restarting my local Galaxy instance today bit it won't start up properly. I keep getting this message when I run "sh run.sh":

Traceback (most recent call last): File "/mnt/ris-fas1a/linux_users/__avnglxy/ris-lx10/galaxy-dist/__lib/galaxy/webapps/galaxy/__buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/mnt/ris-fas1a/linux_users/__avnglxy/ris-lx10/galaxy-dist/__lib/galaxy/app.py", line 79, in __init__ self.datatypes_registry.load___datatypes( self.config.root, self.config.datatypes_config ) File "/mnt/ris-fas1a/linux_users/__avnglxy/ris-lx10/galaxy-dist/__lib/galaxy/datatypes/registry.__py", line 273, in load_datatypes self.to_xml_file() File "/mnt/ris-fas1a/linux_users/__avnglxy/ris-lx10/galaxy-dist/__lib/galaxy/datatypes/registry.__py", line 681, in to_xml_file os.close( fd ) OSError: [Errno 5] Input/output error

The reason for my restart was dur to a users complaint about upload speeds.

Any help is much appreciated! Richard

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