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
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