Hi all,
I found the following Nginx configuration here ( https://github.com/fredhutchio/docker-galaxy/blob/master/nginx.conf ).

Unfortunately, I could not start the docker container ( https://github.com/fredhutchio/docker-galaxy/issues/1 ).

Thank you in advance.

Mic


On Thu, Dec 31, 2015 at 9:33 AM, Mic <mictadlo@gmail.com> wrote:
Hi all,
I found the following Nginx configuration here ( https://github.com/fredhutchio/docker-galaxy/issues/1 ).

Unfortunately, I could not start the docker container ( https://github.com/fredhutchio/docker-galaxy/issues/1 ).

Thank you in advance.

Mic

On Tue, Nov 17, 2015 at 9:32 AM, Eric Rasche <esr@tamu.edu> wrote:
That snippet is no longer needed and was fixed in 15.10.

On 11/16/2015 05:28 PM, Mic wrote:
> 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 <mailto: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>
>     >> <mailto: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>
>     >> <mailto: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>
>     >> <mailto: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>
>     <mailto: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> <mailto: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>
>     >>>>> <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>
>     >>>> <tel:404-692-2048 <tel:404-692-2048>> esr@tamu.edu
>     <mailto:esr@tamu.edu> <mailto: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:
>     >>> 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
esr@tamu.edu