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 greg@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