Hi Mic,

have a look at this page.
https://galaxy.readthedocs.org/en/master/admin/interactive_environments.html

Which version of Galaxy you are using?
Cheers,
Bjoern

Am 11.11.2015 um 11:05 schrieb Mic:
> 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> 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>
>> 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> 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> --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
>>>>> 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/
>>>>
>>>
>>
>>
>