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
>
>
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--
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