Re: [galaxy-dev] Galaxy server broken with install of latest changes
Thanks for the update, glad everything is working as expected!
On Wed, Aug 13, 2014 at 12:27 PM, Tony Kusalik 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 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
> >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
> > e>
> >from framework import expose
> > File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py",
> line 48
> > , in
> >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 y
Re: [galaxy-dev] Galaxy server broken with install of latest changes
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 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
>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
> e>
>from framework import expose
> File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py", line
> 48
> , in
>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/
Re: [galaxy-dev] Galaxy server broken with install of latest changes
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
(/eggs) and start galaxy again. It'll automatically fetch
everything it needs.
-Dannon
On Tue, Aug 12, 2014 at 3:13 PM, Tony Kusalik 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
> 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
> e>
> from framework import expose
> File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py",
> line 48
> , in
> 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/
[galaxy-dev] Galaxy server broken with install of latest changes
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
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
from framework import expose
File "/birl2/Galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 48
, in
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/
