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 <e...@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"
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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
>> e...@tamu.edu
>>
>>
> 
> 
> 
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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> 
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