Galaxy server broken with install of latest changes

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Galaxy server broken with install of latest changes

Tony Kusalik
Hi,

I installed the latest set of changes to Galaxy, and now the Galaxy server will not start up.  I am hoping someone can point me to the source of the problem and/or a fix.

This morning my Galaxy server was running just fine.  I did a
  hg incoming
and was told that a fair number of changes were waiting to be applied,
changeset 13772 through changeset 14309.  Fine.  I did
  hg pull -u
and got
  searching for changes
  adding changesets
  adding manifests
  adding file changes
  added 538 changesets with 1738 changes to 542 files
  473 files updated, 0 files merged, 152 files removed, 0 files unresolved
Fine.
However, now my Galaxy server will not start up and run.  On
  sh run.sh --daemon
the server dies with the following produced in paster.log
where /birl2/Galaxy/galaxy-dist is the name of the installation
directory.

-- begin paster.log --

Traceback (most recent call last):
  File "./scripts/paster.py", line 33, in <module>
    serve.run()
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 10
49, in run
    invoke(command, command_name, options, args[1:])
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 10
55, in invoke
    exit_code = runner.run(args)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 22
0, in run
    result = self.command()
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 64
3, in command
    app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 350, in loadapp
    return loadobj(APP, uri, name=name, **kw)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 374, in loadobj
    global_conf=global_conf)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 399, in loadcontext
    global_conf=global_conf)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 423, in _loadconfig
    return loader.get_context(object_type, name, global_conf)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 561, in get_context
    section)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 620, in _context_from_explicit
    value = import_string(found_expr)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 125, in import_string
    return pkg_resources.EntryPoint.parse("x=" + s).load(False)
  File "/birl2/Galaxy/galaxy-dist/lib/pkg_resources.py", line 1954, in load
    entry = __import__(self.module_name, globals(),globals(), ['__name__'])
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/__init__.py", line 4, in <modul
e>
    from framework import expose
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 48
, in <module>
    eggs.require( "amqp" )
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 414, in req
uire
    raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) )
galaxy.eggs.EggNotFetchable: ['amqp']
Removing PID file paster.pid

-- end paster.log --

The above is the complete content of paster.log.

Anyone have any idea what the problem is?  More importantly, how do I fix the problem
and get Galaxy running again?



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Re: Galaxy server broken with install of latest changes

Dannon Baker-2
Hey Tony,

Thanks for the error report.  I'll look into this, but you can try two things really quickly to see if you can get galaxy started:

1) python scripts/fetch_eggs.py may fix up your egg situation
2) just delete the eggs folder of your galaxy distribution (<galaxy-dist>/eggs) and start galaxy again.  It'll automatically fetch everything it needs.

-Dannon


On Tue, Aug 12, 2014 at 3:13 PM, Tony Kusalik <[hidden email]> wrote:
Hi,

I installed the latest set of changes to Galaxy, and now the Galaxy server will not start up.  I am hoping someone can point me to the source of the problem and/or a fix.

This morning my Galaxy server was running just fine.  I did a
  hg incoming
and was told that a fair number of changes were waiting to be applied,
changeset 13772 through changeset 14309.  Fine.  I did
  hg pull -u
and got
  searching for changes
  adding changesets
  adding manifests
  adding file changes
  added 538 changesets with 1738 changes to 542 files
  473 files updated, 0 files merged, 152 files removed, 0 files unresolved
Fine.
However, now my Galaxy server will not start up and run.  On
  sh run.sh --daemon
the server dies with the following produced in paster.log
where /birl2/Galaxy/galaxy-dist is the name of the installation
directory.

-- begin paster.log --

Traceback (most recent call last):
  File "./scripts/paster.py", line 33, in <module>
    serve.run()
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 10
49, in run
    invoke(command, command_name, options, args[1:])
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 10
55, in invoke
    exit_code = runner.run(args)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 22
0, in run
    result = self.command()
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 64
3, in command
    app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 350, in loadapp
    return loadobj(APP, uri, name=name, **kw)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 374, in loadobj
    global_conf=global_conf)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 399, in loadcontext
    global_conf=global_conf)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 423, in _loadconfig
    return loader.get_context(object_type, name, global_conf)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 561, in get_context
    section)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 620, in _context_from_explicit
    value = import_string(found_expr)
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
 125, in import_string
    return pkg_resources.EntryPoint.parse("x=" + s).load(False)
  File "/birl2/Galaxy/galaxy-dist/lib/pkg_resources.py", line 1954, in load
    entry = __import__(self.module_name, globals(),globals(), ['__name__'])
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/__init__.py", line 4, in <modul
e>
    from framework import expose
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 48
, in <module>
    eggs.require( "amqp" )
  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 414, in req
uire
    raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) )
galaxy.eggs.EggNotFetchable: ['amqp']
Removing PID file paster.pid

-- end paster.log --

The above is the complete content of paster.log.

Anyone have any idea what the problem is?  More importantly, how do I fix the problem
and get Galaxy running again?



___________________________________________________________
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/


___________________________________________________________
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:
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Re: Galaxy server broken with install of latest changes

Tony Kusalik
In reply to this post by Tony Kusalik
My apologies to everyone.  This turns out to be a false alarm.
The problem was caused by a strange, intermittent issue with the
DNS servers on our campus (I'll spare you the gory details).
The problem boiled down to python on my server not being able to
find http://eggs.galaxyproject.org.

On Aug 12, 2014, at 13:13 , Tony Kusalik <[hidden email]> wrote:

> Hi,
>
> I installed the latest set of changes to Galaxy, and now the Galaxy server will not start up.  I am hoping someone can point me to the source of the problem and/or a fix.
>
> This morning my Galaxy server was running just fine.  I did a
>  hg incoming
> and was told that a fair number of changes were waiting to be applied,
> changeset 13772 through changeset 14309.  Fine.  I did
>  hg pull -u
> and got
>  searching for changes
>  adding changesets
>  adding manifests
>  adding file changes
>  added 538 changesets with 1738 changes to 542 files
>  473 files updated, 0 files merged, 152 files removed, 0 files unresolved
> Fine.
> However, now my Galaxy server will not start up and run.  On
>  sh run.sh --daemon
> the server dies with the following produced in paster.log
> where /birl2/Galaxy/galaxy-dist is the name of the installation
> directory.
>
> -- begin paster.log --
>
> Traceback (most recent call last):
>  File "./scripts/paster.py", line 33, in <module>
>    serve.run()
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 10
> 49, in run
>    invoke(command, command_name, options, args[1:])
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 10
> 55, in invoke
>    exit_code = runner.run(args)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 22
> 0, in run
>    result = self.command()
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 64
> 3, in command
>    app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 350, in loadapp
>    return loadobj(APP, uri, name=name, **kw)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 374, in loadobj
>    global_conf=global_conf)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 399, in loadcontext
>    global_conf=global_conf)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 423, in _loadconfig
>    return loader.get_context(object_type, name, global_conf)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 561, in get_context
>    section)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 620, in _context_from_explicit
>    value = import_string(found_expr)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 125, in import_string
>    return pkg_resources.EntryPoint.parse("x=" + s).load(False)
>  File "/birl2/Galaxy/galaxy-dist/lib/pkg_resources.py", line 1954, in load
>    entry = __import__(self.module_name, globals(),globals(), ['__name__'])
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/__init__.py", line 4, in <modul
> e>
>    from framework import expose
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 48
> , in <module>
>    eggs.require( "amqp" )
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 414, in req
> uire
>    raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) )
> galaxy.eggs.EggNotFetchable: ['amqp']
> Removing PID file paster.pid
>
> -- end paster.log --
>
> The above is the complete content of paster.log.
>
> Anyone have any idea what the problem is?  More importantly, how do I fix the problem
> and get Galaxy running again?
>
>
>
> ___________________________________________________________
> 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/


___________________________________________________________
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/
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Re: Galaxy server broken with install of latest changes

Dannon Baker-2
Thanks for the update, glad everything is working as expected!


On Wed, Aug 13, 2014 at 12:27 PM, Tony Kusalik <[hidden email]> wrote:
My apologies to everyone.  This turns out to be a false alarm.
The problem was caused by a strange, intermittent issue with the
DNS servers on our campus (I'll spare you the gory details).
The problem boiled down to python on my server not being able to
find http://eggs.galaxyproject.org.

On Aug 12, 2014, at 13:13 , Tony Kusalik <[hidden email]> wrote:

> Hi,
>
> I installed the latest set of changes to Galaxy, and now the Galaxy server will not start up.  I am hoping someone can point me to the source of the problem and/or a fix.
>
> This morning my Galaxy server was running just fine.  I did a
>  hg incoming
> and was told that a fair number of changes were waiting to be applied,
> changeset 13772 through changeset 14309.  Fine.  I did
>  hg pull -u
> and got
>  searching for changes
>  adding changesets
>  adding manifests
>  adding file changes
>  added 538 changesets with 1738 changes to 542 files
>  473 files updated, 0 files merged, 152 files removed, 0 files unresolved
> Fine.
> However, now my Galaxy server will not start up and run.  On
>  sh run.sh --daemon
> the server dies with the following produced in paster.log
> where /birl2/Galaxy/galaxy-dist is the name of the installation
> directory.
>
> -- begin paster.log --
>
> Traceback (most recent call last):
>  File "./scripts/paster.py", line 33, in <module>
>    serve.run()
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 10
> 49, in run
>    invoke(command, command_name, options, args[1:])
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 10
> 55, in invoke
>    exit_code = runner.run(args)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 22
> 0, in run
>    result = self.command()
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 64
> 3, in command
>    app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 350, in loadapp
>    return loadobj(APP, uri, name=name, **kw)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 374, in loadobj
>    global_conf=global_conf)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 399, in loadcontext
>    global_conf=global_conf)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 423, in _loadconfig
>    return loader.get_context(object_type, name, global_conf)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 561, in get_context
>    section)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 620, in _context_from_explicit
>    value = import_string(found_expr)
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
> 125, in import_string
>    return pkg_resources.EntryPoint.parse("x=" + s).load(False)
>  File "/birl2/Galaxy/galaxy-dist/lib/pkg_resources.py", line 1954, in load
>    entry = __import__(self.module_name, globals(),globals(), ['__name__'])
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/__init__.py", line 4, in <modul
> e>
>    from framework import expose
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 48
> , in <module>
>    eggs.require( "amqp" )
>  File "/birl2/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 414, in req
> uire
>    raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) )
> galaxy.eggs.EggNotFetchable: ['amqp']
> Removing PID file paster.pid
>
> -- end paster.log --
>
> The above is the complete content of paster.log.
>
> Anyone have any idea what the problem is?  More importantly, how do I fix the problem
> and get Galaxy running again?
>
>
>
> ___________________________________________________________
> 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/


___________________________________________________________
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/


___________________________________________________________
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/