Question: error running a local galaxy instance
gravatar for patrick.augereau
4.2 years ago by
patrick.augereau0 wrote:


I installed a local copy of galaxy on my computer (cubuntu 14.04 LTS), because my data volume is too big to allow uploading to in e reasonable time.

I did it in my personal directory, following the direction given in

I choosed the stable branch; btu when I run the command

sh --reload

I get the following error in the term:

<code> ERROR 2014-09-09 11:55:52,496 Error reading tool from path: mutation/visualize.xml
Traceback (most recent call last):
  File "/home/patrick/galaxy-dist/lib/galaxy/tools/", line 576, in load_tool_tag_set
    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
  File "/home/patrick/galaxy-dist/lib/galaxy/tools/", line 692, in load_tool
    tree = load_tool( config_file )
  File "/home/patrick/galaxy-dist/lib/galaxy/tools/", line 13, in load_tool
    tree = raw_tool_xml_tree(path)
  File "/home/patrick/galaxy-dist/lib/galaxy/tools/", line 45, in raw_tool_xml_tree
    tree = parse_xml(path)
  File "/home/patrick/galaxy-dist/lib/galaxy/util/", line 159, in parse_xml
    tree = ElementTree.parse(fname)
  File "/home/patrick/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/", line 859, in parse
    tree.parse(source, parser)
  File "/home/patrick/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/", line 576, in parse
    source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/mutation/visualize.xml'


The script continue to its normal end after that, and I am able to open a local galaxy instance in my firefox browser; but I would like to know if that error could affect latter execution of galaxy tools; especcially, could it affect installation of new tools or genomes via the toolshed.

As a matter of fact, I was able to add tools in a previous install, but unsuccessful in installing drosophilla genome as explained in

Thanks in advance for your help.

ADD COMMENTlink modified 4.2 years ago by Jennifer Hillman Jackson25k • written 4.2 years ago by patrick.augereau0
gravatar for Bjoern Gruening
4.2 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:


this will not affect your Galaxy instance and no other tools. It means that the tool ./tools/mutation/visualize.xml which is defined in your tool_conf.xml file is not available. You should check which tools this is and why you are missing it. Otherwise you can just start your analysis :)



ADD COMMENTlink written 4.2 years ago by Bjoern Gruening5.1k

Thanks Bjoern; this is what I suspected; but as I said, when I want to install a dataset for drosophilla using the administration interface, after adding the appropriate data manager from the toolshed, and executing the tool data_manager_fetch_genome_all_fasta, looking at the result from my history, I have the following error:


Traceback (most recent call last):
  File "/home/patrick/shed_tools/", line 350, in <module>
    if __name__ == "__main__": main()
  File "/home/patrick/shed_tools/", line 345, in main
    REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name )
  File "/home/patrick/shed_tools/", line 182, in download_from_ucsc
    ftp = FTP( UCSC_FTP_SERVER )
  File "/usr/lib/python2.7/", line 120, in __init__
  File "/usr/lib/python2.7/", line 135, in connect
    self.sock = socket.create_connection((, self.port), self.timeout)
  File "/usr/lib/python2.7/", line 571, in create_connection
    raise err
socket.error: [Errno 111] Connection refused


from the last line and two lines before, I understand that the connection timed out; this genome appear to be fetched from UCSC_FTP_SERVER.

I don't know how to correct the problem; but it might be related to the proxy, my computer must use to connect to the internet; in the browser, everything is OK, but I suppose the proxy must be set somewhere in galaxy itself. Do you know where.

Thanks again, for your help or help from anybody.


ADD REPLYlink written 4.2 years ago by patrick.augereau0


this heavily depends on your Galaxy configuration. E.g. if you are running under Apache etc ... usually it is good to have a look at universe_wsgi.xml. Are you able to fetch the genome from command line? If you set the proxy system-wide as default this all should be not a problem.

ADD REPLYlink written 4.2 years ago by Bjoern Gruening5.1k
gravatar for Jennifer Hillman Jackson
4.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


I am not sure if this will help, but here are the wikis for native genome installation. The one you reference above is for Custom Reference Genomes. Be sure to see the linked wikis for Data Mangers and Data Tables.

Best, Jen, Galaxy team

ADD COMMENTlink written 4.2 years ago by Jennifer Hillman Jackson25k

Thanks for your answer; it took me some time to find my way through the various parameters of my computer taking into account the proxy of my lab; finally, I succeeded; this is how I set parameters to this end in case it could help others:

I am running an ubuntu 14.04 computer, behind a proxy; after asking to the people managing the proxy to open the right port (873), I had to set a specific environment variable: RSYNC_PROXY, hence the following command:

export RSYNC_PROXY="numerical address:port number"

For some unknwon reason text address for the proxy did not work; also it is important to remember not to put the protocol before the numerical address (only for textual address); so :

export RSYNC_PROXY="http://numerical address:port number"

is not good, and must be :

export RSYNC_PROXY="numerical address:port number"

and to be sure rsync used the right port, I changed the rsync lines in /etc/services from

rsync    873/tcp

rsync    873/udp

to :

rsync    proxy numerical port/tcp  (udp).


ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by patrick.augereau0
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