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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 <h...@fmi.ch
<mailto:h...@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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