Re: [galaxy-dev] cannot start galaxy after upgade
Hi Greg, Brilliant! Thanks a lot for your advice, it worked! I do run the latest dist release that went out yesterday. Thanks again for your prompt help, it is very much appreciated. Cheers, Anne. On 15 Nov 2012, at 16:45, Greg Von Kuster wrote: > HI Anne, > > Just to confirm, you are running the latest dist release which went out > yesterday, correct? If so, perhaps you can try this: > > %sh manage_tools.sh upgrade > > The above will set the value of the migrate_tools.version column in your > database to the latest migration value. After doing this, try > > %sh run.sh > > which will start up your Galaxy server. Then you can run any of the tool > migrations you want by getting the commands from the Admin menu link. > > Let me know if this works. > > Greg Von Kuster > > On Nov 15, 2012, at 11:39 AM, Anne Pajon wrote: > >> Hi Greg, >> >> No change at all, how can I check? >> >> [webapp@uk-cri-lbio07 galaxy]$ hg status | grep -v '^?' >> M tool-data/shared/ucsc/ucsc_build_sites.txt >> >> The problem may be that I did not upgrade since 14 June 2012. Could it be >> related to the version of tools in the database? Please advice me if you >> could on the places to look at. I've looked at the code but I did not find >> yet which data/config file is causing this error. >> >> Should I revert the upgrade and try to upgrade to the previous release >> instead? Any advices would be very much appreciated. >> >> Thanks. >> Cheers, >> Anne. >> >> >> On 15 Nov 2012, at 16:12, Greg Von Kuster wrote: >> >>> Hi Anne, >>> >>> We've never seen this error before and we are not able to reproduce it, so >>> not sure we can help. Have you made any changes to your Galaxy code base >>> or to your Galaxy environment? >>> >>> Greg Von Kuster >>> >>> On Nov 15, 2012, at 9:15 AM, Anne Pajon wrote: >>> Hi, I'm having some problems restarting our galaxy server after upgrading it to the latest version today... Here is the error message: python path is: /opt/local/home/webapp/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/boto-2.5.2-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/Fabric-1.4.2-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/ssh-1.7.14-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Whoosh-0.3.18-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/amqplib-0.6.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/pexpect-2.4-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg, /opt/local/home/webapp/galaxy/! eggs/Babel-0.9.4-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/Mako-0.4.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/WebHelpers-0.2-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/wchartype-0.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/elementtree-1.2.6_20050316-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/docutils-0.7-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/WebOb-0.8.5-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Routes-1.12.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/PasteDeploy-1.3.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/PasteScript-1.7.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Paste-1.6-py2.7.egg, /opt/local/home/webapp/galaxy/lib, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-pack! ages/setuptools-0.6c11-py2.7.egg, /opt/local/home/webapp/softw! are/p! ython/py thon2.7.2/lib/python2.7/site-packages/MySQL_python-1.2.3-py2.7-linux-x86_64.egg, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/termcolor-1.1.0-py2.7.egg, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/PyYAML-3.10-py2.7-linux-x86_64.egg, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/py_mysql2pgsql-0.1.3-py2.7.egg, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg, /opt/local/home/webapp/software/python/python2.7.2/lib/python27.zip, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/plat-l
Re: [galaxy-dev] cannot start galaxy after upgade
HI Anne, Just to confirm, you are running the latest dist release which went out yesterday, correct? If so, perhaps you can try this: %sh manage_tools.sh upgrade The above will set the value of the migrate_tools.version column in your database to the latest migration value. After doing this, try %sh run.sh which will start up your Galaxy server. Then you can run any of the tool migrations you want by getting the commands from the Admin menu link. Let me know if this works. Greg Von Kuster On Nov 15, 2012, at 11:39 AM, Anne Pajon wrote: > Hi Greg, > > No change at all, how can I check? > > [webapp@uk-cri-lbio07 galaxy]$ hg status | grep -v '^?' > M tool-data/shared/ucsc/ucsc_build_sites.txt > > The problem may be that I did not upgrade since 14 June 2012. Could it be > related to the version of tools in the database? Please advice me if you > could on the places to look at. I've looked at the code but I did not find > yet which data/config file is causing this error. > > Should I revert the upgrade and try to upgrade to the previous release > instead? Any advices would be very much appreciated. > > Thanks. > Cheers, > Anne. > > > On 15 Nov 2012, at 16:12, Greg Von Kuster wrote: > >> Hi Anne, >> >> We've never seen this error before and we are not able to reproduce it, so >> not sure we can help. Have you made any changes to your Galaxy code base or >> to your Galaxy environment? >> >> Greg Von Kuster >> >> On Nov 15, 2012, at 9:15 AM, Anne Pajon wrote: >> >>> Hi, >>> >>> I'm having some problems restarting our galaxy server after upgrading it to >>> the latest version today... >>> >>> Here is the error message: >>> >>> python path is: >>> /opt/local/home/webapp/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, >>> /opt/local/home/webapp/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, >>> /opt/local/home/webapp/galaxy/eggs/boto-2.5.2-py2.7.egg, >>> /opt/local/home/webapp/galaxy/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, >>> /opt/local/home/webapp/galaxy/eggs/Fabric-1.4.2-py2.7.egg, >>> /opt/local/home/webapp/galaxy/eggs/ssh-1.7.14-py2.7.egg, >>> /opt/local/home/webapp/galaxy/eggs/Whoosh-0.3.18-py2.7.egg, >>> /opt/local/home/webapp/galaxy/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, >>> >>> /opt/local/home/webapp/galaxy/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, >>> >>> /opt/local/home/webapp/galaxy/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg, >>> /opt/local/home/webapp/galaxy/eggs/amqplib-0.6.1-py2.7.egg, >>> /opt/local/home/webapp/galaxy/eggs/pexpect-2.4-py2.7.egg, >>> /opt/local/home/webapp/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg, >>> /opt/local/home/webapp/galaxy/e! ggs/Babel-0.9.4-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/Mako-0.4.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/WebHelpers-0.2-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/wchartype-0.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/elementtree-1.2.6_20050316-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/docutils-0.7-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/WebOb-0.8.5-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Routes-1.12.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/PasteDeploy-1.3.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/PasteScript-1.7.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Paste-1.6-py2.7.egg, /opt/local/home/webapp/galaxy/lib, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packa! ges/setuptools-0.6c11-py2.7.egg, /opt/local/home/webapp/softwa! re/p! >>> ython/py >>> thon2.7.2/lib/python2.7/site-packages/MySQL_python-1.2.3-py2.7-linux-x86_64.egg, >>> >>> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/termcolor-1.1.0-py2.7.egg, >>> >>> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/PyYAML-3.10-py2.7-linux-x86_64.egg, >>> >>> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/py_mysql2pgsql-0.1.3-py2.7.egg, >>> >>> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg, >>> /opt/local/home/webapp/software/python/python2.7.2/lib/python27.zip, >>> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7, >>> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/plat-linux2, >>> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-tk, >>> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-old, >>> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-dynload, >>> /opt/local/home/webapp/sof! tware/mercurial/mercurial-2.1/lib/python2.7/site-packages, /opt/local/home/webapp/softwa
Re: [galaxy-dev] cannot start galaxy after upgade
Hi Greg, No change at all, how can I check? [webapp@uk-cri-lbio07 galaxy]$ hg status | grep -v '^?' M tool-data/shared/ucsc/ucsc_build_sites.txt The problem may be that I did not upgrade since 14 June 2012. Could it be related to the version of tools in the database? Please advice me if you could on the places to look at. I've looked at the code but I did not find yet which data/config file is causing this error. Should I revert the upgrade and try to upgrade to the previous release instead? Any advices would be very much appreciated. Thanks. Cheers, Anne. On 15 Nov 2012, at 16:12, Greg Von Kuster wrote: > Hi Anne, > > We've never seen this error before and we are not able to reproduce it, so > not sure we can help. Have you made any changes to your Galaxy code base or > to your Galaxy environment? > > Greg Von Kuster > > On Nov 15, 2012, at 9:15 AM, Anne Pajon wrote: > >> Hi, >> >> I'm having some problems restarting our galaxy server after upgrading it to >> the latest version today... >> >> Here is the error message: >> >> python path is: >> /opt/local/home/webapp/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, >> /opt/local/home/webapp/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, >> /opt/local/home/webapp/galaxy/eggs/boto-2.5.2-py2.7.egg, >> /opt/local/home/webapp/galaxy/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, >> /opt/local/home/webapp/galaxy/eggs/Fabric-1.4.2-py2.7.egg, >> /opt/local/home/webapp/galaxy/eggs/ssh-1.7.14-py2.7.egg, >> /opt/local/home/webapp/galaxy/eggs/Whoosh-0.3.18-py2.7.egg, >> /opt/local/home/webapp/galaxy/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, >> /opt/local/home/webapp/galaxy/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, >> >> /opt/local/home/webapp/galaxy/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg, >> /opt/local/home/webapp/galaxy/eggs/amqplib-0.6.1-py2.7.egg, >> /opt/local/home/webapp/galaxy/eggs/pexpect-2.4-py2.7.egg, >> /opt/local/home/webapp/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg, >> /opt/local/home/webapp/galaxy/eg! gs/Babel-0.9.4-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/Mako-0.4.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/WebHelpers-0.2-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/wchartype-0.1-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/elementtree-1.2.6_20050316-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/docutils-0.7-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/WebOb-0.8.5-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Routes-1.12.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /opt/local/home/webapp/galaxy/eggs/PasteDeploy-1.3.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/PasteScript-1.7.3-py2.7.egg, /opt/local/home/webapp/galaxy/eggs/Paste-1.6-py2.7.egg, /opt/local/home/webapp/galaxy/lib, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packag! es/setuptools-0.6c11-py2.7.egg, /opt/local/home/webapp/softwar! e/p! >> ython/py >> thon2.7.2/lib/python2.7/site-packages/MySQL_python-1.2.3-py2.7-linux-x86_64.egg, >> >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/termcolor-1.1.0-py2.7.egg, >> >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/PyYAML-3.10-py2.7-linux-x86_64.egg, >> >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/py_mysql2pgsql-0.1.3-py2.7.egg, >> >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg, >> /opt/local/home/webapp/software/python/python2.7.2/lib/python27.zip, >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7, >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/plat-linux2, >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-tk, >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-old, >> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-dynload, >> /opt/local/home/webapp/soft! ware/mercurial/mercurial-2.1/lib/python2.7/site-packages, /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages >> galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,841 Loading >> references to tool sheds from tool_sheds_conf.xml >> galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,844 Loaded >> reference to tool shed: Galaxy main tool shed >> galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,844 Loaded >> reference to tool shed: Galaxy test tool shed >> galaxy.model.migrate.check DEBUG 2012-11-15 14:12:54,884 psycopg2 egg >> successfully loaded for postgres dialect >> galaxy.model.migrate.check INFO 2012-11-15 14:12:54,975 At database version >> 107 >> galaxy.tool_she
Re: [galaxy-dev] cannot start galaxy after upgade
Hi Anne,
We've never seen this error before and we are not able to reproduce it, so not
sure we can help. Have you made any changes to your Galaxy code base or to
your Galaxy environment?
Greg Von Kuster
On Nov 15, 2012, at 9:15 AM, Anne Pajon wrote:
> Hi,
>
> I'm having some problems restarting our galaxy server after upgrading it to
> the latest version today...
>
> Here is the error message:
>
> python path is:
> /opt/local/home/webapp/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg,
> /opt/local/home/webapp/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg,
> /opt/local/home/webapp/galaxy/eggs/boto-2.5.2-py2.7.egg,
> /opt/local/home/webapp/galaxy/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg,
> /opt/local/home/webapp/galaxy/eggs/Fabric-1.4.2-py2.7.egg,
> /opt/local/home/webapp/galaxy/eggs/ssh-1.7.14-py2.7.egg,
> /opt/local/home/webapp/galaxy/eggs/Whoosh-0.3.18-py2.7.egg,
> /opt/local/home/webapp/galaxy/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg,
> /opt/local/home/webapp/galaxy/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg,
>
> /opt/local/home/webapp/galaxy/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg,
> /opt/local/home/webapp/galaxy/eggs/amqplib-0.6.1-py2.7.egg,
> /opt/local/home/webapp/galaxy/eggs/pexpect-2.4-py2.7.egg,
> /opt/local/home/webapp/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg,
> /opt/local/home/webapp/galaxy/egg!
s/Babel-0.9.4-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/Mako-0.4.1-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/WebHelpers-0.2-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/wchartype-0.1-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/elementtree-1.2.6_20050316-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/docutils-0.7-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/WebOb-0.8.5-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/Routes-1.12.3-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/PasteDeploy-1.3.3-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/PasteScript-1.7.3-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/Paste-1.6-py2.7.egg,
/opt/local/home/webapp/galaxy/lib,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-package!
s/setuptools-0.6c11-py2.7.egg, /opt/local/home/webapp/software!
/p!
> ython/py
> thon2.7.2/lib/python2.7/site-packages/MySQL_python-1.2.3-py2.7-linux-x86_64.egg,
>
> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/termcolor-1.1.0-py2.7.egg,
>
> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/PyYAML-3.10-py2.7-linux-x86_64.egg,
>
> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/py_mysql2pgsql-0.1.3-py2.7.egg,
>
> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg,
> /opt/local/home/webapp/software/python/python2.7.2/lib/python27.zip,
> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7,
> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/plat-linux2,
> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-tk,
> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-old,
> /opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-dynload,
> /opt/local/home/webapp/softw!
are/mercurial/mercurial-2.1/lib/python2.7/site-packages,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages
> galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,841 Loading
> references to tool sheds from tool_sheds_conf.xml
> galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,844 Loaded
> reference to tool shed: Galaxy main tool shed
> galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,844 Loaded
> reference to tool shed: Galaxy test tool shed
> galaxy.model.migrate.check DEBUG 2012-11-15 14:12:54,884 psycopg2 egg
> successfully loaded for postgres dialect
> galaxy.model.migrate.check INFO 2012-11-15 14:12:54,975 At database version
> 107
> galaxy.tool_shed.migrate.check DEBUG 2012-11-15 14:12:54,991 psycopg2 egg
> successfully loaded for postgres dialect
> Traceback (most recent call last):
> File "/opt/local/home/webapp/galaxy/lib/galaxy/webapps/galaxy/buildapp.py",
> line 36, in app_factory
>app = UniverseApplication( global_conf = global_conf, **kwargs )
> File "/opt/local/home/webapp/galaxy/lib/galaxy/app.py", line 47, in __init__
>verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
> '__file__', None ), self.config.database_engine_options )
> File "/opt/local/home/webapp/galaxy/lib/galaxy/tool_shed/migrate/check.py",
> line 56, in verify_tools
>tool_shed_accessible, missing_tool_configs_dict = check_f
[galaxy-dev] cannot start galaxy after upgade
Hi,
I'm having some problems restarting our galaxy server after upgrading it to the
latest version today...
Here is the error message:
python path is:
/opt/local/home/webapp/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/boto-2.5.2-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/Fabric-1.4.2-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/ssh-1.7.14-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/Whoosh-0.3.18-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/amqplib-0.6.1-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/pexpect-2.4-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/!
Babel-0.9.4-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/Mako-0.4.1-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/WebHelpers-0.2-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/wchartype-0.1-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/elementtree-1.2.6_20050316-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/docutils-0.7-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/WebOb-0.8.5-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/Routes-1.12.3-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg,
/opt/local/home/webapp/galaxy/eggs/PasteDeploy-1.3.3-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/PasteScript-1.7.3-py2.7.egg,
/opt/local/home/webapp/galaxy/eggs/Paste-1.6-py2.7.egg,
/opt/local/home/webapp/galaxy/lib,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/!
setuptools-0.6c11-py2.7.egg, /opt/local/home/webapp/software/p!
ython/py
thon2.7.2/lib/python2.7/site-packages/MySQL_python-1.2.3-py2.7-linux-x86_64.egg,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/termcolor-1.1.0-py2.7.egg,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/PyYAML-3.10-py2.7-linux-x86_64.egg,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/py_mysql2pgsql-0.1.3-py2.7.egg,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg,
/opt/local/home/webapp/software/python/python2.7.2/lib/python27.zip,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/plat-linux2,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-tk,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-old,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/lib-dynload,
/opt/local/home/webapp/softwar!
e/mercurial/mercurial-2.1/lib/python2.7/site-packages,
/opt/local/home/webapp/software/python/python2.7.2/lib/python2.7/site-packages
galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,841 Loading
references to tool sheds from tool_sheds_conf.xml
galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,844 Loaded
reference to tool shed: Galaxy main tool shed
galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-15 14:12:54,844 Loaded
reference to tool shed: Galaxy test tool shed
galaxy.model.migrate.check DEBUG 2012-11-15 14:12:54,884 psycopg2 egg
successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2012-11-15 14:12:54,975 At database version 107
galaxy.tool_shed.migrate.check DEBUG 2012-11-15 14:12:54,991 psycopg2 egg
successfully loaded for postgres dialect
Traceback (most recent call last):
File "/opt/local/home/webapp/galaxy/lib/galaxy/webapps/galaxy/buildapp.py",
line 36, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/opt/local/home/webapp/galaxy/lib/galaxy/app.py", line 47, in __init__
verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File "/opt/local/home/webapp/galaxy/lib/galaxy/tool_shed/migrate/check.py",
line 56, in verify_tools
tool_shed_accessible, missing_tool_configs_dict = check_for_missing_tools(
app, tool_panel_configs, latest_tool_migration_script_number )
File "/opt/local/home/webapp/galaxy/lib/galaxy/tool_shed/migrate/common.py",
line 46, in check_for_missing_tools
tool_dependencies_dict = tool_shed_decode( text )
File "/opt/local/home/webapp/galaxy/lib/galaxy/tool_shed/encoding_util.py",
line 15, in tool_shed_decode
a, b = value.sp
