Hi John,

We are using Apache with the following configuration:

#Configuration file for galaxy

<VirtualHost *:80>

        #ServerName localhost:80

        ServerName X.X.X:80  #I have commented out our serverName for the purpose of this email

DocumentRoot /mnt/workspace/DATA/galaxy

RewriteEngine on

#RewriteRule ^/galaxy$ /galaxy/ [R]

RewriteRule ^/static/style/(.*) /galaxy-dist/static/june_2007_style/blue/$1 [L]

RewriteRule ^/static/scripts/(.*) /galaxy-dist/static/scripts/packed/$1 [L]

RewriteRule ^/static/(.*) /galaxy-dist/static/$1 [L]

RewriteRule ^/favicon.ico /galaxy-dist/static/favicon.ico [L]

RewriteRule ^/robots.txt /galaxy-dist/static/robots.txt [L]

RewriteRule ^(.*) http://localhost:8080$1 [P]

        <Directory /mnt/workspace/DATA/galaxy>

         #      Options +Includes

               #Order allow,deny

Order deny,allow

Deny from All

                Allow from X.X.X  #I have commented out our subnet for the purpose of this email

               #Allow from All

        </Directory>

</Virtualhost>

Thanks in advance for any suggestions,

Audrey

On Tue, Aug 19, 2014 at 8:53 PM, John Chilton <jmchilton@gmail.com> wrote:

Hello Audrey,

  Please keep responses on list - it ensures people smarter than me
can respond :). Can you tell me what is sitting in front of Galaxy -
Apache, Nginx, uwsgi, etc... and send the configurations if possible?
I believe the out-of-the-box uwsgi configuration has some problems
with really long URL query strings which using the tool shed does
produce.

-John

On Mon, Aug 18, 2014 at 11:56 AM, audrey michel <audreymannion@gmail.com> wrote:
> Hi John,
>
> We tried the following on another server where there is no proxy, and we are
> able to install tools from this new instance:
>
>
> hg clone https://bitbucket.org/galaxy/galaxy-dist/
>
>
>  $ hg clone https://bitbucket.org/galaxy/galaxy-dist/
> destination directory: galaxy-dist
> requesting all changes
> adding changesets
> adding manifests
> adding file changes
> added 14316 changesets with 48369 changes to 8546 files (+1 heads)
> updating to branch default
> 3597 files updated, 0 files merged, 0 files removed, 0 files unresolved
>
> We then modified just the admin_users, tool_dependency_dir, port and
> localhost. This was sufficient to allow us to use the toolshed to install
> tools on this particular instance of galaxy.
>
> So it would appear to be a proxy issue with our other instance of galaxy
> which is behind a proxy. Could you advise us on where we need to add
> http_proxy as we don't know which file(s) to add this to? We already set the
> filter-with = proxy-prefix in the universe_wsgi.ini fiel.
>
> Thanks in advance,
> Audrey
>
>
>
>
>
>
>
>
> On Mon, Aug 18, 2014 at 11:31 AM, audrey michel <audreymannion@gmail.com>
> wrote:
>>
>> Hi John,
>>
>> Thanks for the suggestions. We are going to try a new install on one of
>> our other servers and see if the problem occurs there or not.
>>
>> Will update you when we do this.
>>
>> Thanks.
>> Audrey
>>
>>
>> On Fri, Aug 15, 2014 at 8:20 PM, John Chilton <jmchilton@gmail.com> wrote:
>>>
>>> Okay - I am replying in thread but I not to your original message
>>> because there might be private stuff in the log you sent me. It looks
>>> like you were trying to install fastqdump from the main tool shed. So
>>> I setup a fresh Galaxy instance this morning and the only two things I
>>> changed in the universe_wsgi.ini file were admin_users and
>>> tool_dependency_dir (required to install tool dependencies) and this
>>> install worked for me. Your error message had "Bad Status Line" in it
>>> - so it sounds like you were getting non-sense back from the tool
>>> shed.
>>>
>>> This could be because there is some proxy interfering with this
>>> request, it could be that it was just an intermittent problem with the
>>> tool shed, or ... some configuration problem potentially? I am not
>>> sure.
>>>
>>> It looks like you had cloned galaxy-dist directly - I think it is
>>> better to stay on a particular branch - I would do this:
>>>
>>> hg pull
>>> hg update latest_2014.08.11
>>>
>>> To make sure you have the latest and greatest Galaxy and then retry?
>>>
>>> If you still have problems and it is the same strack trace - please
>>> let me know. Next up would be to eliminate the proxy theory - not sure
>>> how to do that though :(.
>>>
>>> -John
>>>
>>> On Wed, Aug 13, 2014 at 4:36 PM, John Chilton <jmchilton@gmail.com>
>>> wrote:
>>> > I am not sure what the problem is - more details would really help.
>>> > For instance - What version of Galaxy are you using? What repository
>>> > are you trying to install? Do other repositories work? Does the Galaxy
>>> > log have a more complete stack trace?
>>> >
>>> > Any additional details would be most helpful.
>>> >
>>> > Thanks,
>>> > -John
>>> >
>>> > On Tue, Aug 12, 2014 at 9:11 AM, audrey michel
>>> > <audreymannion@gmail.com> wrote:
>>> >> Hi,
>>> >>
>>> >> We get the following error when we try to install any tool from the
>>> >> Tool
>>> >> shed when using the Admin panel:
>>> >>
>>> >>
>>> >> Internal Server Error
>>> >>
>>> >> Galaxy was unable to successfully complete your request
>>> >>
>>> >> An error occurred.
>>> >>
>>> >> This may be an intermittent problem due to load or other unpredictable
>>> >> factors, reloading the page may address the problem.
>>> >>
>>> >> The error has been logged to our team.
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> We would be grateful if you could advise on this issue.
>>> >>
>>> >> Kind Regards,
>>> >> Audrey Michel
>>> >> Baranov Lab
>>> >> School of Biochemistry & Cell Biology
>>> >> University College Cork
>>> >> Ireland
>>> >>
>>> >>
>>> >>
>>> >> ___________________________________________________________
>>> >> 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/
>>> >>
>>> >> To search Galaxy mailing lists use the unified search at:
>>> >>   http://galaxyproject.org/search/mailinglists/
>>
>>
>