Thanks Peter- I'll make sure to update the tool shed wiki accordingly as soon 
as possible.

Greg Von Kuster


On Jan 31, 2013, at 9:48 AM, Peter Cock wrote:

> On Thu, Jan 31, 2013 at 2:40 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> 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
>> 
> 
> Looks like Galaxy was using Python 2.7, and that does seem to be able
> to fetch all the eggs. Progress:
> 
> $ tail -n 50 community_webapp.log
> galaxy.tools DEBUG 2013-01-31 14:43:30,552 Loading section: SNP/WGA:
> QC; LD; Plots
> galaxy.tools DEBUG 2013-01-31 14:43:30,552 Loading section: SNP/WGA:
> Statistical Models
> galaxy.tools DEBUG 2013-01-31 14:43:30,552 Loading section: Phenotype
> Association
> galaxy.tools DEBUG 2013-01-31 14:43:30,553 Loading section: VCF Tools
> Tool shed hgweb.config file is:
> /Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/hgweb.config
> galaxy.web.framework.base DEBUG 2013-01-31 14:43:30,903 Enabling
> 'admin' controller, class: AdminController
> galaxy.web.framework.base DEBUG 2013-01-31 14:43:30,910 Enabling 'hg'
> controller, class: HgController
> galaxy.web.framework.base DEBUG 2013-01-31 14:43:30,910 Enabling
> 'repository' controller, class: RepositoryController
> galaxy.web.framework.base DEBUG 2013-01-31 14:43:30,918 Enabling
> 'repository_review' controller, class: RepositoryReviewController
> galaxy.web.framework.base DEBUG 2013-01-31 14:43:30,926 Enabling
> 'upload' controller, class: UploadController
> galaxy.web.framework.base DEBUG 2013-01-31 14:43:30,927 Enabling
> 'user' controller, class: User
> galaxy.webapps.community.buildapp DEBUG 2013-01-31 14:43:30,930
> Enabling 'httpexceptions' middleware
> galaxy.webapps.community.buildapp DEBUG 2013-01-31 14:43:30,930
> Enabling 'recursive' middleware
> galaxy.webapps.community.buildapp DEBUG 2013-01-31 14:43:30,932
> Enabling 'print debug' middleware
> galaxy.webapps.community.buildapp DEBUG 2013-01-31 14:43:30,946
> Enabling 'error' middleware
> galaxy.webapps.community.buildapp DEBUG 2013-01-31 14:43:30,947
> Enabling 'trans logger' middleware
> galaxy.webapps.community.buildapp DEBUG 2013-01-31 14:43:30,947
> Enabling 'config' middleware
> galaxy.webapps.community.buildapp DEBUG 2013-01-31 14:43:30,947
> Enabling 'x-forwarded-host' middleware
> mercurial version is: 2.2.3
> Traceback (most recent call last):
>  File "./scripts/paster.py", line 34, in <module>
>    command.run()
>  File 
> "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
> line 84, in run
>    invoke(command, command_name, options, args[1:])
>  File 
> "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
> line 123, in invoke
>    exit_code = runner.run(args)
>  File 
> "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
> line 218, in run
>    result = self.command()
>  File 
> "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
> line 276, in command
>    relative_to=base, global_conf=vars)
>  File 
> "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
> line 313, in loadapp
>    **kw)
>  File 
> "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
> line 204, in loadapp
>    return loadobj(APP, uri, name=name, **kw)
>  File 
> "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
> line 225, in loadobj
>    return context.create()
>  File 
> "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
> line 625, in create
>    return self.object_type.invoke(self)
>  File 
> "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
> line 110, in invoke
>    return fix_call(context.object, context.global_conf, **context.local_conf)
>  File 
> "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/util/fixtypeerror.py",
> line 57, in fix_call
>    val = callable(*args, **kw)
>  File 
> "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/webapps/community/buildapp.py",
> line 72, in app_factory
>    webapp = wrap_in_middleware( webapp, global_conf, **kwargs )
>  File 
> "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/webapps/community/buildapp.py",
> line 157, in wrap_in_middleware
>    app = hg.Hg( app, conf )
>  File 
> "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/webapps/community/framework/middleware/hg.py",
> line 30, in __init__
>    self.db_url = "sqlite:///%s?isolation_level=IMMEDIATE" %
> self.config[ 'database_file' ]
> KeyError: 'database_file'
> Removing PID file community_webapp.pid
> 
> I noticed that the community_wsgi.ini.sample file had database_file
> as a commented out line:
> 
> #database_file = database/community.sqlite
> 
> I expected that to be used as the default value - commenting it got
> the tool shed to run. Perhaps the wiki page needs clarifying on this?
> http://wiki.galaxyproject.org/HostingALocalToolShed
> 
> Regards,
> 
> Peter
> ___________________________________________________________
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