Hi Zachary, On Dec 8, 2011, at 10:11 AM, Zachary Charlop-Powers wrote:

Greg,

I thought I sent the e-mail below last night. Sorry. I reinstalled Galaxy and ran into the same issue. Since I can modify my own tools and the Toolsheds are not strictly necessary for what we are doing I am going to stop trying for a bit. I am a little confused that it doesn't work, however, and wonder if there is not an issue in one of the scripts. I don't know which script would be responsible for making a local copy of the Galaxy Toolshed tools but when I "grep" for "repository" in the /galaxy-dist/ folder the only non-template file you get is lib/galaxy/webapps/community/controllers/repository.py I glanced through that file but I didn't see a part of the script that had the exact order of the error message I was receiving - but perhaps I didn't know the file very well?

It seems you have a bit of a misunderstanding about the main Galaxy tool shed (http://toolshed.g2.bx.psu.edu/), and the mercurial repositories that are available in it as well as the motivation for hosting your own local Galaxy tool shed. The mercurial repositories that are currently available in the main Galaxy tool shed can be "hg cloned" individually or "automatically installed" individually as a means of making their contents (Galaxy tools, workflows, data, etc) available to your local Galaxy instance. So if you configure and host your own local Galaxy tool shed, your shed will not initially contain anything until you add your own locally developed tools to it. Starting up a local tool shed does not result in the mercurial repositories currently available in the main galaxy tool shed being automatically made available in the local tool shed. The intent of the main Galaxy tool shed is to enable sharing of tools between the many local Galaxy instances around the globe. But again, the mercurial repositories containing these tools must be individually installed into your local Galaxy instance. There are many way to go about doing this - all documented in the tool shed wiki at http://wiki.g2.bx.psu.edu/Tool%20Shed. This provides flexibility to those hosting their own local Galaxy instances in that they can install only those tools in which they have interest, and are not forced to get all of them in order to get any one of them. In the near future, we will begin to move the tools currently included in the Galaxy distribution to the Galaxy main tool shed.

In any event I agree with you that it is not a server error nor a community_wsgi.ini error (since I didn't do anything to them in this new install) but something small in the setup where the repository is not being told the correct location to install its tools. If you have any suggestions I am happy to try some small things but I have to give up for a bit because its amazing how much time you can spend tracking these things down.

I would strongly suggest that you eliminate the use of proxying Galaxy behind apache as your proxy configuration is certainly the cause of the issues you are seeing.

thanks again for your time and your efforts to the creation of this great tool. zach cp

Greg,

I've been looking very carefully at http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_... to make sure that I have been doing this right.

After encountering the initial error (directory not found) I :

1. prematurely attempted to setup a local Galaxy toolshed. 2. started to get a new series of issues related to community_wsgi.ini and nginx.conf.

Clearly this was incorrect and I can restore the default configuration of these files. However the initial error which is that default Galaxy installation procedure did not allow me to use the main Galaxy Toolshed Tools remains. According to the webpage above this should be a very simple procedure, akin to the main Galaxy setup.

I think the best thing to do is to do a totally clean install, use the Apache config files you guys have included for port forwarding and not mess with any other files. If that is the case I should be able to install Galaxy Tools via the web without starting up a second server. I think thats probably the best way to proceed - not too hard since I don;t really have any data or history on the server yet.

Just clean out the galaxy user home folder, create a new Postgresql database and configure Apache. If I still have problems after that I will let you know.

thanks Greg, zach cp

On Dec 7, 2011, at 12:18 PM, Greg Von Kuster wrote:

...

Based on the following requests from the bottom of your paster log, you are attempting to access the Galaxy main tool shed, not a locally running tool shed. SInce this is the case, you do not need to do anything with community_wsgi.ini!

serving on http://127.0.0.1:8080 129.85.185.149 - - [07/Dec/2011:11:46:11 -0400] "GET / HTTP/1.0" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:10.0a2) Gecko/20111206 Firefox/10.0a2" 129.85.185.149 - - [07/Dec/2011:11:46:11 -0400] "GET /history HTTP/1.0" 200 - "http://bradybeast/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:10.0a2) Gecko/20111206 Firefox/10.0a2" 129.85.185.149 - - [07/Dec/2011:11:46:11 -0400] "GET /root/tool_menu HTTP/1.0" 200 - "http://bradybeast/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:10.0a2) Gecko/20111206 Firefox/10.0a2" 129.85.185.149 - - [07/Dec/2011:11:46:11 -0400] "POST /root/user_get_usage HTTP/1.0" 200 - "http://bradybeast/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:10.0a2) Gecko/20111206 Firefox/10.0a2" 129.85.185.149 - - [07/Dec/2011:11:46:17 -0400] "GET /admin HTTP/1.0" 200 - "http://bradybeast/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:10.0a2) Gecko/20111206 Firefox/10.0a2" 129.85.185.149 - - [07/Dec/2011:11:46:17 -0400] "GET /admin/center?status=done&message=&webapp=galaxy HTTP/1.0" 200 - "http://bradybeast/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:10.0a2) Gecko/20111206 Firefox/10.0a2" 129.85.185.149 - - [07/Dec/2011:11:46:37 -0400] "GET /admin/browse_tool_sheds HTTP/1.0" 200 - "http://bradybeast/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:10.0a2) Gecko/20111206 Firefox/10.0a2" 129.85.185.149 - - [07/Dec/2011:11:46:38 -0400] "GET /admin/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.0" 302 - "http://bradybeast/admin/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:10.0a2) Gecko/20111206 Firefox/10.0a2"

If you are trying to get your requests to proxy to something like /galaxy/bradybeast/... then you need to uncomment the following filter-with setting in your universe_wsgi.ini file. You will also need to configure your nginx the same way. Make sure to follow the directions precisely as documented in our wiki at http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy.

# If running behind a proxy server and Galaxy is served from a subdirectory, # enable the proxy-prefix filter and set the prefix in the # [filter:proxy-prefix] section above. #filter-with = proxy-prefix

On Dec 7, 2011, at 10:49 AM, Zachary Charlop-Powers wrote:

...

Sure. I'm the same guy who was on the IRC yesterday.

thanks again for your time. zach cp

<community_wsgi.ini><universe_wsgi.ini>

On Dec 7, 2011, at 10:35 AM, Greg Von Kuster wrote:

...

Hello Zach,

Are you trying to get a local install of Galaxy to communicate with a local tool shed? If so, can you send me your universe_wsgi.ini file and your community_wsgi.ini file?

Greg Von Kuster

On Dec 7, 2011, at 10:20 AM, Zachary Charlop-Powers wrote:

...

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

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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu

Greg Von Kuster Galaxy Development Team greg@bx.psu.edu

Greg Von Kuster Galaxy Development Team greg@bx.psu.edu