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 <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?
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 <kusalik@cs.usask.ca> 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?
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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 <kusalik@cs.usask.ca> 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/
Thanks for the update, glad everything is working as expected! On Wed, Aug 13, 2014 at 12:27 PM, Tony Kusalik <kusalik@cs.usask.ca> 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 <kusalik@cs.usask.ca> 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/
participants (2)
-
Dannon Baker -
Tony Kusalik