Hi all After the announcements this morning, I upgraded to the latest stable release as suggested (latest_2015.01.13). Our server is now not starting with the following error message. Any ideas what I might be doing wrong? Thanks a lot Ulf --- galaxy.eggs DEBUG 2015-01-14 14:10:25,272 Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.6.egg galaxy.eggs ERROR 2015-01-14 14:10:25,290 One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution. galaxy.eggs ERROR 2015-01-14 14:10:25,291 Dependency "bioblend" requires "mock" Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run result = self.command() File "/home/galaxy/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 "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 375, in loadobj return context.create() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 813, in create return self.object_type.invoke(self) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 249, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call val = callable(*args, **kw) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 54, in app_factory webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py", line 119, in add_ui_controllers module = import_module( module_name ) File "/home/galaxy/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py", line 37, in import_module __import__(name) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py", line 21, in <module> eggs.require('bioblend') File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 411, in require return c[req.project_name].require() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 239, in require dists = self.resolve() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 170, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/home/galaxy/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 (/home/galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.6.egg), Requirement.parse('mock')) --- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
Hi all For what it's worth, I manually installed mock (and pycrypto because that was the next thing it complained about) and it worked after that. Ulf On 14/01/15 14:23, Ulf Schaefer wrote:
Hi all
After the announcements this morning, I upgraded to the latest stable release as suggested (latest_2015.01.13).
Our server is now not starting with the following error message. Any ideas what I might be doing wrong?
Thanks a lot Ulf
---
galaxy.eggs DEBUG 2015-01-14 14:10:25,272 Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.6.egg galaxy.eggs ERROR 2015-01-14 14:10:25,290 One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution. galaxy.eggs ERROR 2015-01-14 14:10:25,291 Dependency "bioblend" requires "mock" Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run result = self.command() File "/home/galaxy/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 "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 375, in loadobj return context.create() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 813, in create return self.object_type.invoke(self) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 249, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call val = callable(*args, **kw) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 54, in app_factory webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py", line 119, in add_ui_controllers module = import_module( module_name ) File "/home/galaxy/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py", line 37, in import_module __import__(name) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py", line 21, in <module> eggs.require('bioblend') File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 411, in require return c[req.project_name].require() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 239, in require dists = self.resolve() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 170, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/home/galaxy/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 (/home/galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.6.egg), Requirement.parse('mock'))
---
************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ************************************************************************** ___________________________________________________________ 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: https://lists.galaxyproject.org/
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************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
Sorry for the delayed response - I am not really an expert on Galaxy's egg stuff - but I believe running `python scripts/fetch_eggs.py` before starting Galaxy usually fixes these problems for reasons I don't understand. One probably shouldn't need to manually install mock or pycrypto though. Sorry for the problems and thanks for using Galaxy (and upgrading)! -John On Thu, Jan 15, 2015 at 10:42 AM, Ulf Schaefer <Ulf.Schaefer@phe.gov.uk> wrote:
Hi all
For what it's worth, I manually installed mock (and pycrypto because that was the next thing it complained about) and it worked after that.
Ulf
On 14/01/15 14:23, Ulf Schaefer wrote:
Hi all
After the announcements this morning, I upgraded to the latest stable release as suggested (latest_2015.01.13).
Our server is now not starting with the following error message. Any ideas what I might be doing wrong?
Thanks a lot Ulf
---
galaxy.eggs DEBUG 2015-01-14 14:10:25,272 Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.6.egg galaxy.eggs ERROR 2015-01-14 14:10:25,290 One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution. galaxy.eggs ERROR 2015-01-14 14:10:25,291 Dependency "bioblend" requires "mock" Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run result = self.command() File "/home/galaxy/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 "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 375, in loadobj return context.create() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 813, in create return self.object_type.invoke(self) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 249, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call val = callable(*args, **kw) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 54, in app_factory webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py", line 119, in add_ui_controllers module = import_module( module_name ) File "/home/galaxy/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py", line 37, in import_module __import__(name) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py", line 21, in <module> eggs.require('bioblend') File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 411, in require return c[req.project_name].require() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 239, in require dists = self.resolve() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 170, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/home/galaxy/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 (/home/galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.6.egg), Requirement.parse('mock'))
---
************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ************************************************************************** ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ************************************************************************** ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
-
John Chilton -
Ulf Schaefer