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 usegalaxy.org in e reasonable time.
I did it in my personal directory, following the direction given in https://wiki.galaxyproject.org/Admin/GetGalaxy.
I choosed the stable branch; btu when I run the command
sh run.sh --reload
I get the following error in the term:
galaxy.tools 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/__init__.py", 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/__init__.py", line 692, in load_tool
tree = load_tool( config_file )
File "/home/patrick/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = raw_tool_xml_tree(path)
File "/home/patrick/galaxy-dist/lib/galaxy/tools/loader.py", line 45, in raw_tool_xml_tree
tree = parse_xml(path)
File "/home/patrick/galaxy-dist/lib/galaxy/util/__init__.py", line 159, in parse_xml
tree = ElementTree.parse(fname)
File "/home/patrick/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
File "/home/patrick/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", 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 https://wiki.galaxyproject.org/Learn/CustomGenomes.
Thanks in advance for your help.