Question: Error After Upgrade
gravatar for Farhat Habib
8.2 years ago by
Farhat Habib80
Farhat Habib80 wrote:
Dear All, After upgrading using hg pull -u -r f09915c8da94 then, hg diff after which it asked me to upgrade db which I did using, sh upgrade Galaxy fails to start on my local install. galaxy.model.custom_types DEBUG 2010-09-13 11:41:18,475 pysqlite>=2 egg successfully loaded for sqlite dialect Traceback (most recent call last): File "/home/farhat/galaxy-central/lib/galaxy/web/", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/farhat/galaxy-central/lib/galaxy/", line 42, in __init__ self.tool_data_tables = self.config.tool_data_table_config_path ) File "/home/farhat/galaxy- central/lib/galaxy/tools/data/", line 22, in __init__ self.add_from_config_file( config_filename ) File "/home/farhat/galaxy- central/lib/galaxy/tools/data/", line 31, in add_from_config_file tree = util.parse_xml( config_filename ) File "/home/farhat/galaxy-central/lib/galaxy/util/", line 101, in parse_xml tree = ElementTree.parse(fname) File "/home/farhat/galaxy-central/eggs/elementtree-1.2.6_20050316-py 2.6.egg/elementtree/", line 859, in parse tree.parse(source, parser) File "/home/farhat/galaxy-central/eggs/elementtree-1.2.6_20050316-py 2.6.egg/elementtree/", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tool_data_table_conf.xml' Any help with rectifying this? Yours, -Farhat
galaxy • 1.2k views
ADD COMMENTlink modified 8.2 years ago by Brad Chapman240 • written 8.2 years ago by Farhat Habib80
gravatar for Brad Chapman
8.2 years ago by
Brad Chapman240
United States
Brad Chapman240 wrote:
Farhat; [...] [...] There is a new configuration file 'tool_data_table_conf.xml.' In your main galaxy directory, you can add this manually with: cp tool_data_table_conf.xml.sample tool_data_table_conf.xml or re-run Hope this helps, Brad
ADD COMMENTlink written 8.2 years ago by Brad Chapman240
Thanks, rerunning worked. -Farhat -- Farhat Habib, PhD IISER Fellow, Biology Indian Institute of Science Education & Research, Sai Trinity Building, Garware Circle, Sutarwadi, Pashan, Pune-411 021. Office: +91 20 2590 8015
ADD REPLYlink written 8.2 years ago by Farhat Habib80
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