Hi Mic,
I'm not entirely sure what you are searching for.
You already used this one right?
https://github.com/bgruening/docker-galaxy-stable
Docker and IPython should work here.
You will find a nginx.conf included in this as well or you can use the
ansible playrole here with all describtions on howto setup a Galaxy
instance with nginx.
https://github.com/galaxyproject/ansible-galaxy-extras
Ciao,
Bjoern
Am 31.12.2015 um 00:37 schrieb Mic:
> 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
>>>
>>>
>>
>