[galaxy-dev] Tool Shed Automatic Install Behind NGINX Proxy
Hello Galaxy Team/Users, Thanks again for your great work. A few months back I setup a local Galaxy server behind Nginx and everything worked great except for the browser-based automatic-install of tools from Galaxy-main. Using the web interface I would click on Install to local Galaxy and get the following error message: The resource could not be found. No route for /repository/Noneadmin_toolshed/install_repository At the time I had absolutely no idea where the problem came from and the very helpful dev team assisted me in tracking the issue to a problem with the proxy configuration, however I was never able to resolve the issue despite tinkering with the proxy configuration. Since I need the proxy (on a computer with other web-facing services) and since I could install tools using mercurial I didn't follow up the issue, however, automatic-install of tools would be great to have. A similar error is in the archives for someone using Apache (http://galaxy-development-list-archive.2308389.n4.nabble.com/Toolshed-not-accessible-td4096102.html ) and when I e-mailed the author he said he hadn't been able to resolve the issue and had simply worked around it as I had. As my Galaxy setup is very straightforward and follows the Galaxy Wiki instructions, I am thinking that others must have encountered this same problem, so here is my question: 1. For users who have installed Galaxy and use either the Apache or Nginx proxy configuration from the Wiki, have you gotten the browser-based Automatic Install of toolshed tools to work? 2. If so - could you share your proxy setup with me? best, zach cp Zach Charlop-Powers Post-Doctoral Fellow Laboratory of Genetically Encoded Small Molecules Rockefeller University zchar...@rockefeller.edu ___ 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/
Re: [galaxy-dev] Tool Shed Automatic Install Behind NGINX Proxy
Thanks Greg, I've already updated to the latest Galaxy-dist but can try Galaxy-central. I was hoping some others out there might have some insight into the issue but if its already fixed that would be great. thanks, zach cp On Mar 2, 2012, at 3:26 PM, Greg Von Kuster wrote: Hello Zach, If your Galaxy instance is not current, make sure to update with with the latest as issues in this area have been corrected. I haven't heard any issues related to this from anyone in the community, but that's not to say that there aren't any remaining. I'm not sure how many in the community that have this environment are using the tool shed. Greg Von Kuster On Mar 2, 2012, at 3:14 PM, Zachary Charlop-Powers wrote: Hello Galaxy Team/Users, Thanks again for your great work. A few months back I setup a local Galaxy server behind Nginx and everything worked great except for the browser-based automatic-install of tools from Galaxy-main. Using the web interface I would click on Install to local Galaxy and get the following error message: The resource could not be found. No route for /repository/Noneadmin_toolshed/install_repository At the time I had absolutely no idea where the problem came from and the very helpful dev team assisted me in tracking the issue to a problem with the proxy configuration, however I was never able to resolve the issue despite tinkering with the proxy configuration. Since I need the proxy (on a computer with other web-facing services) and since I could install tools using mercurial I didn't follow up the issue, however, automatic-install of tools would be great to have. A similar error is in the archives for someone using Apache (http://galaxy-development-list-archive.2308389.n4.nabble.com/Toolshed-not-accessible-td4096102.html ) and when I e-mailed the author he said he hadn't been able to resolve the issue and had simply worked around it as I had. As my Galaxy setup is very straightforward and follows the Galaxy Wiki instructions, I am thinking that others must have encountered this same problem, so here is my question: 1. For users who have installed Galaxy and use either the Apache or Nginx proxy configuration from the Wiki, have you gotten the browser-based Automatic Install of toolshed tools to work? 2. If so - could you share your proxy setup with me? best, zach cp Zach Charlop-Powers Post-Doctoral Fellow Laboratory of Genetically Encoded Small Molecules Rockefeller University zchar...@rockefeller.edumailto:zchar...@rockefeller.edu ___ 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/ Zach Charlop-Powers Post-Doctoral Fellow Laboratory of Genetically Encoded Small Molecules Rockefeller University zchar...@rockefeller.edumailto:zchar...@rockefeller.edu ___ 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/
[galaxy-dev] manage_db.sh error
Hi Galaxy Team, I am running a small local instance of Galaxy and I've run into a database error following an upgrade to the Jan27th galaxy-dist release. The last line when I run run.sh tells me to upgrade my database: Exception: Your database has version '85' but this code expects version '90'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. But when I run the manage_db.sh I run into the following errors: $ sh manage_db.sh Traceback (most recent call last): File ./scripts/manage_db.py, line 12, in module from migrate.versioning.shell import main File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/shell.py, line 7, in module from migrate.versioning.base import * File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/base/__init__.py, line 5, in module from const import databases,operations File /home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/base/const.py, line 7, in module from sqlalchemy.util import OrderedDict ImportError: No module named sqlalchemy.util The first thing that pops out is that I the sqlalchemy egg is part of py2.7 while I am using python2.6. Any suggestions on how to troubleshoot this? thanks, zach cp ___ 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/
[galaxy-dev] Configuring Toolsheds
Hello Galaxy, I have been having trouble getting Toolsheds to work on a local install of Galaxy. Based on the error messages I think that I have not correctly modified the nginx server port forwarding and/or the community_wsgi.ini file. If anyone has successfully setup a local toolshed repository I would love to hear from you. thanks zach cp ___ 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/
