Hi all, I was hoping to make some enhancements to the ToolShed, so first I need to be able to run my own ToolShed locally:
http://wiki.galaxyproject.org/HostingALocalToolShed I have the latest code for bitbucket for galaxy-central: $ hg heads default changeset: 9117:04e221996871 user: Greg Von Kuster <g...@bx.psu.edu> date: Wed Jan 30 16:47:20 2013 -0500 summary: Dont' assume a complex repository dependency was properly defined. The following cryptic error is not helpful: $ sh run_community.sh Command 'serve' not known (you may need to run setup.py egg_info) No commands registered. Have you installed Paste Script? (try running python setup.py develop) I then noticed that there was no community_wsgi.ini file, and tried using a copy of the sample: $ cp community_wsgi.ini.sample community_wsgi.ini $ sh run_community.sh (runs with no output, finished in 3s) Does it make sense to generate community_wsgi.ini automatically? Or give an explicit error if it is missing? Looking at the log file, I have a Python depenancy issue here: $ more community_webapp.log ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/builds.txt' ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/publicbuilds.txt' ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ensembl/builds.txt' ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ncbi/builds.txt' WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Traceback (most recent call last): File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/webapps/community/buildapp.py", line 56, in app_factory from galaxy.webapps.community.app import UniverseApplication File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/webapps/community/app.py", line 2, in <module> from galaxy import tools File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/tools/__init__.py", line 36, in <module> import galaxy.util.shed_util_common File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/shed_util_common.py", line 27, in <module> eggs.require( 'markupsafe' ) File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/eggs/__init__.py", line 413, in require return pkg_resources.working_set.require( req_str ) File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/pkg_resources.py", line 666, in require needed = self.resolve(parse_requirements(requirements)) File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here DistributionNotFound: markupsafe Removing PID file community_webapp.pid Should this work under Mac OS X? I suspect there are some eggs missing on the Galaxy site which would be needed: $ python2.6 ./scripts/fetch_eggs.py Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: ssh (a dependent egg of Fabric) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 37, in <module> c.resolve() # Only fetch eggs required by the config File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Regards, Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
