Hi Chris,

(1) Galaxy configuration has been moved to /config/galaxy.ini
(
https://bitbucket.org/galaxy/galaxy-dist/src/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb/config/
)

(2) There might have been some changes to the conf syntax regarding the
dependency directory etc. since the version of universe.wsgi.ini that you
are using.  So please make sure you are using the current galaxy.ini file
and try installing a tool again. If it does not go well please include the
log of errors.

Let us know how it goes.

Thanks

Martin

On Tue, Oct 7, 2014 at 3:50 PM, Chris Dagdigian <d...@sonsorol.org> wrote:

>
> Hi folks,
>
> Got a strange problem - it's hit me on all my self-install options today
> including using the Chef cookbook as well as the galaxy mecurial install
> method on Ubuntu 12.04 LTS
>
> I'm trying to build a local galaxy that supports a few common extra
> tools (things like samtools etc.)
>
> I can boot a fresh Ubuntu 12.04 LTS and follow the instructions at
> getgalaxy.org:
>
> >   hg clone https://bitbucket.org/galaxy/galaxy-dist/
> >   cd galaxy-dist
> >   hg update stable
>      sh ./run.sh
>
>
> There are two strange things that don't quite match what I'm expecting
> to see from the docs ...
>
> (1)  The file "universe_wsgi.ini " no longer gets created in
> galaxy-dist/  after running "run.sh" for the first time. This is strange
> because I remember it working days ago but now on fresh server and fresh
> checkout the file does not get created and I have to manually create one
> in oder to set "host = 0.0.0.0"
>
> (2) I can't even install simple tools like samtools from the standard
> tool sheds. The status page gets stuck at "installing dependencies" and
> if I navigate away I get a browser javascript error ("Initializing
> repository installation failed"
>
> Any tips or tricks appreciated, thanks!
>
> Regards,
> Chris
>
>
>
>
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