new user : galaxy install error

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new user : galaxy install error

Abhishek Pratap
**Did the following**

hg clone https://bitbucket.org/galaxy/galaxy-dist/ test
cd test/
hg update stable


Machine:
Mac Yosemite(10.10.1)


**Got the following error**


Some eggs are out of date, attempting to fetch...
Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
Traceback (most recent call last):
  File "./scripts/fetch_eggs.py", line 46, in <module>
    c.resolve() # Only fetch eggs required by the config
  File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
line 347, in resolve
    egg.resolve()
  File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
line 192, in resolve
    if e.args[1].key != e.args[0].key:
IndexError: tuple index out of range
Fetch failed.


Traceback (most recent call last):
  File "./scripts/paster.py", line 33, in <module>
    serve.run()
  File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py",
line 1049, in run
    invoke(command, command_name, options, args[1:])
  File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py",
line 1055, in invoke
    exit_code = runner.run(args)
  File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py",
line 220, in run
    result = self.command()
  File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py",
line 643, in command
    app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
  File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
line 350, in loadapp
    return loadobj(APP, uri, name=name, **kw)
  File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
line 375, in loadobj
    return context.create()
  File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
line 813, in create
    return self.object_type.invoke(self)
  File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
line 249, in invoke
    return fix_call(context.object, context.global_conf, **context.local_conf)
  File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
line 97, in fix_call
    val = callable(*args, **kw)
  File "/Users/apratap/softwares/test/lib/galaxy/webapps/galaxy/buildapp.py",
line 54, in app_factory
    webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
  File "/Users/apratap/softwares/test/lib/galaxy/web/framework/webapp.py",
line 119, in add_ui_controllers
    module = import_module( module_name )
  File "/Users/apratap/softwares/test/lib/galaxy/util/backports/importlib/__init__.py",
line 37, in import_module
    __import__(name)
  File "/Users/apratap/softwares/test/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py",
line 21, in <module>
    eggs.require('bioblend')
  File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
line 411, in require
    return c[req.project_name].require()
  File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
line 239, in require
    dists = self.resolve()
  File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
line 170, in resolve
    dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
  File "/Users/apratap/softwares/test/lib/pkg_resources.py", line 569,
in resolve
    raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/Users/apratap/softwares/test/eggs/bioblend-0.4.2-py2.7.egg),
Requirement.parse('poster'))
galaxy.jobs.handler INFO 2015-01-16 16:40:58,095 sending stop signal
to worker thread
galaxy.jobs.handler INFO 2015-01-16 16:40:58,096 job handler queue stopped
galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LWRRunner: Sending
stop signal to monitor thread
galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LWRRunner: Sending
stop signal to 3 worker threads
galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LocalRunner: Sending
stop signal to 5 worker threads
galaxy.jobs.handler INFO 2015-01-16 16:40:58,097 sending stop signal
to worker thread
galaxy.jobs.handler INFO 2015-01-16 16:40:58,098 job handler stop queue stopped
___________________________________________________________
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Re: new user : galaxy install error

saketkc
It probably happens due to a system installed package conflict.
You should probably do it inside a virtual environment:

virtualenv --no-site-packages venv
source venv/bin/activate
cd galaxy-dist
sh run.sh

That should hopefully solve the problem.

On 16 January 2015 at 16:42, Abhishek Pratap <[hidden email]> wrote:

> **Did the following**
>
> hg clone https://bitbucket.org/galaxy/galaxy-dist/ test
> cd test/
> hg update stable
>
>
> Machine:
> Mac Yosemite(10.10.1)
>
>
> **Got the following error**
>
>
> Some eggs are out of date, attempting to fetch...
> Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
> Traceback (most recent call last):
>   File "./scripts/fetch_eggs.py", line 46, in <module>
>     c.resolve() # Only fetch eggs required by the config
>   File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
> line 347, in resolve
>     egg.resolve()
>   File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
> line 192, in resolve
>     if e.args[1].key != e.args[0].key:
> IndexError: tuple index out of range
> Fetch failed.
>
>
> Traceback (most recent call last):
>   File "./scripts/paster.py", line 33, in <module>
>     serve.run()
>   File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py",
> line 1049, in run
>     invoke(command, command_name, options, args[1:])
>   File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py",
> line 1055, in invoke
>     exit_code = runner.run(args)
>   File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py",
> line 220, in run
>     result = self.command()
>   File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py",
> line 643, in command
>     app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
>   File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
> line 350, in loadapp
>     return loadobj(APP, uri, name=name, **kw)
>   File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
> line 375, in loadobj
>     return context.create()
>   File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
> line 813, in create
>     return self.object_type.invoke(self)
>   File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
> line 249, in invoke
>     return fix_call(context.object, context.global_conf, **context.local_conf)
>   File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py",
> line 97, in fix_call
>     val = callable(*args, **kw)
>   File "/Users/apratap/softwares/test/lib/galaxy/webapps/galaxy/buildapp.py",
> line 54, in app_factory
>     webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
>   File "/Users/apratap/softwares/test/lib/galaxy/web/framework/webapp.py",
> line 119, in add_ui_controllers
>     module = import_module( module_name )
>   File "/Users/apratap/softwares/test/lib/galaxy/util/backports/importlib/__init__.py",
> line 37, in import_module
>     __import__(name)
>   File "/Users/apratap/softwares/test/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py",
> line 21, in <module>
>     eggs.require('bioblend')
>   File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
> line 411, in require
>     return c[req.project_name].require()
>   File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
> line 239, in require
>     dists = self.resolve()
>   File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py",
> line 170, in resolve
>     dists = pkg_resources.working_set.resolve( (
> self.distribution.as_requirement(), ), env, self.fetch )
>   File "/Users/apratap/softwares/test/lib/pkg_resources.py", line 569,
> in resolve
>     raise VersionConflict(dist,req) # XXX put more info here
> pkg_resources.VersionConflict: (bioblend 0.4.2
> (/Users/apratap/softwares/test/eggs/bioblend-0.4.2-py2.7.egg),
> Requirement.parse('poster'))
> galaxy.jobs.handler INFO 2015-01-16 16:40:58,095 sending stop signal
> to worker thread
> galaxy.jobs.handler INFO 2015-01-16 16:40:58,096 job handler queue stopped
> galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LWRRunner: Sending
> stop signal to monitor thread
> galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LWRRunner: Sending
> stop signal to 3 worker threads
> galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LocalRunner: Sending
> stop signal to 5 worker threads
> galaxy.jobs.handler INFO 2015-01-16 16:40:58,097 sending stop signal
> to worker thread
> galaxy.jobs.handler INFO 2015-01-16 16:40:58,098 job handler stop queue stopped
> ___________________________________________________________
> 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/
___________________________________________________________
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/