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:
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>>> 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
>>
>>
>
>
>
> ___________________________________________________________
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>