Hi all,
Thank you for the link. I did not know about the link.

@Bjoern: Few month back I saw somewhere a website where it was possible to
download a VM with Galaxy. By any chance, do you remember the link?

Thank you in advance.

Mic

On Wed, Nov 11, 2015 at 10:29 PM, Björn Grüning <bjoern.gruen...@gmail.com>
wrote:

> Hi Mic,
>
> have a look at this page.
>
> https://galaxy.readthedocs.org/en/master/admin/interactive_environments.html
>
> Which version of Galaxy you are using?
> Cheers,
> Bjoern
>
> Am 11.11.2015 um 11:05 schrieb Mic:
> > Hi all,
> > Is there any log files which could show what did go wrong or is there any
> > documentation how to install IEs?
> >
> > Thank you in advance.
> >
> > Mic
> >
> > On Mon, Nov 9, 2015 at 9:12 AM, Mic <micta...@gmail.com> wrote:
> >
> >> 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.gruen...@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 <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"
> >>>>>> 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/
> >>>>
> >>>
> >>
> >>
> >
>
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