Error starting Galaxy after update of March 2012
Hi, I run upgrade: hg pull -u -r 40f1816d6857 on our local instance, and I'm now unable to start Galaxy.. Here is the content of Galaxy_log: Traceback (most recent call last): File "<galaxy_dir>/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "<galaxy_dir>/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.objectstore import build_object_store_from_config File "<galaxy_dir>/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 27, in <module> from galaxy.objectstore.s3_multipart_upload import multipart_upload File "<galaxy_dir>/galaxy-dist/lib/galaxy/objectstore/s3_multipart_upload.py", line 22, in <module> eggs.require('boto') File "<galaxy_dir>/galaxy-dist/lib/galaxy/eggs/__init__.py", line 415, in require raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) ) EggNotFetchable: ['boto'] Removing PID file <galaxy_dir>/galaxy-dist/galaxy.pid Is that an error specific to our instance? Is there a way to downgrade Galaxy? Thanks by advance for your answer.. Alban -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
On Mar 13, 2012, at 10:36 AM, Alban Lermine wrote:
Hi,
I run upgrade: hg pull -u -r 40f1816d6857 on our local instance, and I'm now unable to start Galaxy..
Here is the content of Galaxy_log:
Traceback (most recent call last): File "<galaxy_dir>/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "<galaxy_dir>/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.objectstore import build_object_store_from_config File "<galaxy_dir>/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 27, in <module> from galaxy.objectstore.s3_multipart_upload import multipart_upload File "<galaxy_dir>/galaxy-dist/lib/galaxy/objectstore/s3_multipart_upload.py", line 22, in <module> eggs.require('boto') File "<galaxy_dir>/galaxy-dist/lib/galaxy/eggs/__init__.py", line 415, in require raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) ) EggNotFetchable: ['boto'] Removing PID file <galaxy_dir>/galaxy-dist/galaxy.pid
Is that an error specific to our instance?
Hi Alban, Is your Galaxy server behind a firewall or without network access such that it cannot access http://eggs.g2.bx.psu.edu/ ? What happens if you run `python scripts/fetch_eggs.py` by hand?
Is there a way to downgrade Galaxy?
Yes, in most cases you can downgrade with `hg update -r <old changeset id>`. --nate
Thanks by advance for your answer..
Alban
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
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Nate Coraor wrote:
On Mar 13, 2012, at 10:36 AM, Alban Lermine wrote:
Hi,
I run upgrade: hg pull -u -r 40f1816d6857 on our local instance, and I'm now unable to start Galaxy..
Here is the content of Galaxy_log:
Traceback (most recent call last): File "<galaxy_dir>/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "<galaxy_dir>/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.objectstore import build_object_store_from_config File "<galaxy_dir>/galaxy-dist/lib/galaxy/objectstore/__init__.py", line 27, in <module> from galaxy.objectstore.s3_multipart_upload import multipart_upload File "<galaxy_dir>/galaxy-dist/lib/galaxy/objectstore/s3_multipart_upload.py", line 22, in <module> eggs.require('boto') File "<galaxy_dir>/galaxy-dist/lib/galaxy/eggs/__init__.py", line 415, in require raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) ) EggNotFetchable: ['boto'] Removing PID file <galaxy_dir>/galaxy-dist/galaxy.pid
Is that an error specific to our instance?
Hi Alban,
Is your Galaxy server behind a firewall or without network access such that it cannot access http://eggs.g2.bx.psu.edu/ ?
What happens if you run `python scripts/fetch_eggs.py` by hand?
Is there a way to downgrade Galaxy?
Yes, in most cases you can downgrade with `hg update -r <old changeset id>`.
--nate
Thanks by advance for your answer..
Alban
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
___________________________________________________________ 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:
Re, Thanks for your fast answer.. I run fetch_eggs.py by hand, here is the return: Fetched http://eggs.g2.bx.psu.edu/boto/boto-2.2.2-py2.6.egg Removed conflicting egg: <galaxy_dir>/galaxy-dist/eggs/boto-1.8d-py2.6.egg I tried then to start Galaxy, and I also have a new error message: Traceback (most recent call last): File "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/app.py", line 24, in __init__ self.config.check() File "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/config.py", line 254, in check raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) ) ConfigurationError: Unable to create missing directory: ./../shed_tools [Errno 13] Permission denied: './../shed_tools' It seems it's now only a permission problem.. (I only have rights on galaxy-dist directory), I will ask our system engineer to rerun update.. Alban -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
On Mar 13, 2012, at 11:08 AM, Alban Lermine wrote:
Hi Alban,
Is your Galaxy server behind a firewall or without network access such that it cannot access http://eggs.g2.bx.psu.edu/ ?
What happens if you run `python scripts/fetch_eggs.py` by hand?
Is there a way to downgrade Galaxy?
Yes, in most cases you can downgrade with `hg update -r <old changeset id>`.
--nate
Thanks by advance for your answer..
Alban
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
___________________________________________________________ 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:
Re,
Thanks for your fast answer..
I run fetch_eggs.py by hand, here is the return:
Fetched http://eggs.g2.bx.psu.edu/boto/boto-2.2.2-py2.6.egg Removed conflicting egg: <galaxy_dir>/galaxy-dist/eggs/boto-1.8d-py2.6.egg
I tried then to start Galaxy, and I also have a new error message:
Traceback (most recent call last): File "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/app.py", line 24, in __init__ self.config.check() File "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/config.py", line 254, in check raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) ) ConfigurationError: Unable to create missing directory: ./../shed_tools [Errno 13] Permission denied: './../shed_tools'
It seems it's now only a permission problem.. (I only have rights on galaxy-dist directory), I will ask our system engineer to rerun update..
Hi Alban, You can fix this one by changing the path to the shed_tools directory in shed_tool_conf.xml. It can be any directory you can write to, but should not be underneath the galaxy-dist directory. --nate
Alban
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
Nate Coraor wrote:
On Mar 13, 2012, at 11:08 AM, Alban Lermine wrote:
Hi Alban,
Is your Galaxy server behind a firewall or without network access such that it cannot access http://eggs.g2.bx.psu.edu/ ?
What happens if you run `python scripts/fetch_eggs.py` by hand?
Is there a way to downgrade Galaxy?
Yes, in most cases you can downgrade with `hg update -r <old changeset id>`.
--nate
Thanks by advance for your answer..
Alban
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
___________________________________________________________ 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:
Re,
Thanks for your fast answer..
I run fetch_eggs.py by hand, here is the return:
Fetched http://eggs.g2.bx.psu.edu/boto/boto-2.2.2-py2.6.egg Removed conflicting egg: <galaxy_dir>/galaxy-dist/eggs/boto-1.8d-py2.6.egg
I tried then to start Galaxy, and I also have a new error message:
Traceback (most recent call last): File "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/app.py", line 24, in __init__ self.config.check() File "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/config.py", line 254, in check raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) ) ConfigurationError: Unable to create missing directory: ./../shed_tools [Errno 13] Permission denied: './../shed_tools'
It seems it's now only a permission problem.. (I only have rights on galaxy-dist directory), I will ask our system engineer to rerun update..
Hi Alban,
You can fix this one by changing the path to the shed_tools directory in shed_tool_conf.xml. It can be any directory you can write to, but should not be underneath the galaxy-dist directory.
--nate
Alban
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
It's working again, great thanks, Alban -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
participants (2)
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Alban Lermine -
Nate Coraor