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