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_shed_repository_tools_into_a_local_Galaxy_instance
> 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 t
