Bioblend dependency error
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
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-oth... 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.sidiro@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/
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.baker@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-oth...
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.sidiro@gmail.com <javascript:_e(%7B%7D,'cvml','nikos.sidiro@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 evan@msi.umn.edu boll0107@umn.edu
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 <boll0107@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.baker@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-oth...
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.sidiro@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 evan@msi.umn.edu boll0107@umn.edu
Dannon, `python scripts/fetch_eggs.py` failed with errors about more packages (pycrypto, poster). After installing them and running the 'fetch_eggs' script successfully I'm getting this error upon starting the server: galaxy.eggs ERROR 2014-06-04 16:20:40,694 Dependency "bioblend" requires "simplejson" 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('simplejson')) Simplejson is installed in the system and the library folder is in the galaxy user's PYTHONPATH. On 4 June 2014 15:32, Evan Bollig <boll0107@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.baker@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-oth...
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.sidiro@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 evan@msi.umn.edu boll0107@umn.edu
So the problem now is that you have conflicting eggs on your system path that are getting loaded prior to the galaxy supplied eggs. Galaxy manages its own dependencies, and not relying on those installed via pip/etc. The simplest, most fool-proof solution here is to use a virtualenv and start galaxy in a clean environment. See the virtualenv bit here: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer Basically, you're going to want to: pip install virtualenv virtualenv env_galaxy_clean source env_galaxy_clean/bin/activate sh run.sh (or otherwise launch galaxy from within this new environment) On Wed, Jun 4, 2014 at 10:25 AM, Nikos Sidiropoulos <nikos.sidiro@gmail.com> wrote:
Dannon,
`python scripts/fetch_eggs.py` failed with errors about more packages (pycrypto, poster).
After installing them and running the 'fetch_eggs' script successfully I'm getting this error upon starting the server:
galaxy.eggs ERROR 2014-06-04 16:20:40,694 Dependency "bioblend" requires "simplejson"
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('simplejson'))
Simplejson is installed in the system and the library folder is in the galaxy user's PYTHONPATH.
On 4 June 2014 15:32, Evan Bollig <boll0107@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.baker@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-oth...
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.sidiro@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 evan@msi.umn.edu boll0107@umn.edu
participants (3)
-
Dannon Baker -
Evan Bollig -
Nikos Sidiropoulos