Most of them include at least at little documentation in the code, and the egg ones are documented here: https://wiki.galaxyproject.org/Admin/Config/Eggs
There's not (that I know of or could find) a single wiki page documenting all scripts, but that's not a bad idea. On Wed, Jun 4, 2014 at 9:32 AM, Evan Bollig <boll0...@umn.edu> wrote: > Dannon, > > Do you guys have a web page that documents all of the script/ utilities? I > know most of my deployment and upgrade problems have been resolved by > various scripts in there, but I have no idea what's available until I turn > to this mailing list. > > -E > > > On Wednesday, June 4, 2014, Dannon Baker <dannon.ba...@gmail.com> wrote: > >> Hey Nikos, >> >> I think you're seeing the same issue from this trello card here: >> https://trello.com/c/HWuxsftB/1596-fetching-zip-safe-eggs-that-depend-on-other-eggs-will-fail >> >> Can you run `python scripts/fetch_eggs.py` from your galaxy directory? >> That should re-fetch galaxy's eggs and you should be up and running again. >> >> >> On Wed, Jun 4, 2014 at 9:15 AM, Nikos Sidiropoulos < >> nikos.sid...@gmail.com> wrote: >> >>> Hi all, >>> >>> after the latest galaxy update I've experienced the following error >>> while trying to start the server. >>> >>> galaxy.eggs DEBUG 2014-06-04 14:34:56,027 Fetched >>> http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg >>> galaxy.eggs ERROR 2014-06-04 14:34:56,047 One of Galaxy's managed eggs >>> depends on something which is missing, this is almost certainly a bug in t >>> he egg distribution. >>> galaxy.eggs ERROR 2014-06-04 14:34:56,047 Dependency "bioblend" requires >>> "mock" >>> Traceback (most recent call last): >>> File "./scripts/paster.py", line 33, in <module> >>> serve.run() >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py", >>> line 1049, in run >>> invoke(command, command_name, options, args[1:]) >>> File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util >>> /pastescript/serve.py", line 1055, in invoke >>> exit_code = runner.run(args) >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py", >>> line 220, in run >>> result = self.command() >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py", >>> line 643, in command >>> app = loadapp( app_spec, name=app_name, relative_to=base, >>> global_conf=vars) >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", >>> line 350, in loadapp >>> return loadobj(APP, uri, name=name, **kw) >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", >>> line 375, in loadobj >>> return context.create() >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", >>> line 813, in create >>> return self.object_type.invoke(self) >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", >>> line 249, in invoke >>> return fix_call(context.object, context.global_conf, >>> **context.local_conf) >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", >>> line 97, in fix_call >>> val = callable(*args, **kw) >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", >>> line 49, in app_factory >>> webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/web/framework/__init__.py", >>> line 441, in add_ui_controllers >>> module = import_module( module_name ) >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py", >>> line 37, in import_module >>> __import__(name) >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py", >>> line 20, in <module> >>> eggs.require('bioblend') >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py", >>> line 409, in require >>> return c[req.project_name].require() >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py", >>> line 237, in require >>> dists = self.resolve() >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py", >>> line 168, in resolve >>> dists = pkg_resources.working_set.resolve( ( >>> self.distribution.as_requirement(), ), env, self.fetch ) >>> File >>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/pkg_resources.py", >>> line 569, in resolve >>> raise VersionConflict(dist,req) # XXX put more info here >>> pkg_resources.VersionConflict: (bioblend 0.4.2 >>> (/steno-internal/projects/galaxy-test/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg), >>> Requirement.parse('mock')) >>> >>> >>> First I got and error about the python module 'requests' missing, fixed >>> it using 'pip install', and then got the error above. >>> >>> Regards, >>> Nikos >>> >>> ___________________________________________________________ >>> 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/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> > > -- > -Evan Bollig > Research Associate | Application Developer | User Support Consultant > Minnesota Supercomputing Institute > 599 Walter Library > 612 624 1447 > e...@msi.umn.edu > boll0...@umn.edu > >
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