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
e...@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/

Reply via email to