Hi all,
Thank you for your email, I found on the bottom of this site https://wiki.galaxyproject.org/Admin/Config/nginxProxy a configuration for IE, but I am not quite sure whether it is enough. To update the documentation would be really awesome.

Thank you in advance.

Mic

On Tue, Nov 17, 2015 at 12:05 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Nate configured it on Galaxy main last week, maybe I can convince him to
update the documentation ...


> Hi Mic,
>
> Yes... neither of us use Nginx as our primary proxy, so we never
> wrote the configuration for it.
>
> If you use Nginx I'm assuming you're familiar with its configuration.
> As you can see from the apache route, you really just need a few
> proxy_pass statements. If you can write those, we'd be more than
> happy to include them in our documentation.
>
> Ciao, Eric
>
>
> On 11/16/2015 07:44 AM, Mic wrote:
>> Hi all, Looking at this link
>> (http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html)
>>
>>
it seem Nginx configuration is missing.
>>
>> How to configure Nginx for IE and Galaxy 15.10?
>>
>> Thank you in advance.
>>
>> Mic
>>
>> On Thu, Nov 12, 2015 at 2:36 AM, Eric Rasche <esr@tamu.edu
>> <mailto:esr@tamu.edu>> wrote:
>>
>> Hi Mic,
>>
>> Replying off list as this seems to be a different set of issues
>> than others experience.
>>
>> 1) From your earlier mails it sounded like you had been reading
>> the docs on GIEs, but you asked for then here. Have you read
>> through
>> http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html
>>
>>
yet? If so, how far did you get?
>>
>> 2) do you have docker installed? what version? ("docker -v" I
>> believe)
>>
>> 3) What release of Galaxy are you on? The instructions are version
>> specific in places.
>>
>> 3) All of the files for GIEs are in
>> config/plugins/interactive_environments. Have you made any changes
>> to your local ipython.ini or rstudio.ini?
>>
>> Any logs from GIEs will appear in your normal Galaxy logs. E.g.
>> paster.log
>>
>> Ciao, Eric
>>
>> 11. nov. 2015 10.05 a.m. skrev Mic <mictadlo@gmail.com
>> <mailto:mictadlo@gmail.com>>:
>>
>> Hi all, Is there any log files which could show what did go wrong
>> or is there any documentation how to install IEs?
>>
>> Thank you in advance.
>>
>> Mic
>>
>> On Mon, Nov 9, 2015 at 9:12 AM, Mic <mictadlo@gmail.com
>> <mailto:mictadlo@gmail.com>> wrote:
>>
>> Hi Bjoern, Thank you for your email. I tried the attached Annovar
>> output which is tabular separated. Unfortunately, Rstudio and
>> Ipython still did not show up.
>>
>> Thank you in advance.
>>
>> Best wishes,
>>
>> Mic
>>
>> On Sat, Nov 7, 2015 at 9:58 AM, Björn Grüning
>> <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>>
>> wrote:
>>
>> Hi Mic,
>>
>> please check any other file than a VCF file. Try a txt file for
>> example.
>>
>> Thanks, Bjoern
>>
>> Am 07.11.2015 um 00:54 schrieb Mic:
>>> Hi Eric, I added your line to ipython.xml and rstudio.xml and
>> restarted Galaxy, but
>>> still Rstudio and Ipython do not appear on my test.vcf
>> file by clicking the
>>> *visualize* icon.
>>>
>>> <test type="isinstance" test_attr="datatype"
>>> result_type="datatype">tabular.Tabular</test> <test
>>> type="isinstance" test_attr="datatype"
>>> result_type="datatype">data.Text</test> *<test type="isinstance"
>>> test_attr="datatype" result_type="datatype">tabular.VCF</test>*
>>>
>>> What did I miss?
>>>
>>> Thank you in advance.
>>>
>>> Mic
>>>
>>> On Sat, Nov 7, 2015 at 1:13 AM, Eric Rasche
>> <esr@tamu.edu <mailto:esr@tamu.edu>> wrote:
>>>
>>>> Hi Mic,
>>>>
>>>> I don't believe GIEs are currently activated for
>> anything other than plain
>>>> text and tabular files. You can edit the
>>>>
>> $GALAXY_ROOT/config/plugins/interactive_environments/ipython/config/ipython.xml
>>
>>  (and rstudio/config/rstudio.xml) files to add a line like:
>>>>
>>>> Konsole output <test type="isinstance" test_attr="datatype"
>>>> result_type="datatype">tabular.VCF</test>
>>>>
>>>> and that /should/ let you open VCF files. (I haven't
>> tested that exact
>>>> datatype but I believe that should work). GIEs have
>> been somewhat
>>>> experimental so far, so we haven't felt the need to
>> expand which datatypes
>>>> they apply to lest we overwhelm/surprise users.
>>>>
>>>> Ciao, Eric
>>>>
>>>>
>>>>
>>>>
>>>> On 11/06/2015 02:56 AM, Mic wrote:
>>>>> Hello, Last week, I cloned Galaxy from Github. I uploaded a
>> VCF file from my
>>>>> computer. I also installed the following additional
>> software:
>>>>>
>>>>> /apt-key adv --keyserver keyserver.ubuntu.com
>> <http://keyserver.ubuntu.com>
>>>>> <http://keyserver.ubuntu.com> --recv-keys E084DAB9/ /echo
>>>>> 'deb
>> http://cran.r-project.org/bin/linux/ubuntu trusty/' >>
>>>>> /etc/apt/sources.list/ /apt-get -qq update && apt-get
>>>>> install
>> --no-install-recommends -y
>>>>> libcurl4-openssl-dev libxml2-dev/ /apt-get install
>>>>> apt-transport-https python-dev
>> libc-dev pandoc
>>>>> pkg-config liblzma-dev libbz2-dev libpcre3-dev/ /apt-get
>>>>> install libblas-dev liblapack-dev gfortran
>> libzmq3-dev curl/
>>>>> /apt-get install libfreetype6-dev libpng-dev
>> net-tools procps r-base
>>>>> libreadline-dev / /pip install distribute --upgrade/ /pip
>>>>> install scipy sklearn-pandas bioblend
>> matplotlib patsy pysam khmer
>>>>> ggplot mpld3 sympy rpy2/ /pip install pyzmq ipython==2.4
>>>>> jinja2 tornado
>> pygments numpy biopython
>>>>> scikit-learn pandas/
>>>>>
>>>>> However, clicking the /visualize/ icon no iPython
>> and RStudio are
>>>>> visible. Galaxy is in my home folder installed
>> //home/lorencm/galaxy./
>>>>>
>>>>> What am I missing?
>>>>>
>>>>> Thank you in advance.
>>>>>
>>>>> Mic
>>>>>
>>>>>
>>>>>
>> ___________________________________________________________
>>>>> 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:
>>>>> https://lists.galaxyproject.org/
>>>>>
>>>>> To search Galaxy mailing lists use the unified
>> search at:
>>>>> http://galaxyproject.org/search/mailinglists/
>>>>>
>>>>
>>>> -- Eric Rasche Programmer II
>>>>
>>>> Center for Phage Technology Rm 312A, BioBio Texas A&M
>>>> University College Station, TX 77843 404-692-2048
>>>> <tel:404-692-2048> esr@tamu.edu <mailto:esr@tamu.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:
>>> https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
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>>>
>>
>>
>>
>>
>