30 Dec
2015
30 Dec
'15
6:33 p.m.
Hi all, I found the following Nginx configuration here ( https://github.com/fredhutchio/docker-galaxy/issues/1 ).
Unfortunately, I could not start the docker container ( https://github.com/fredhutchio/docker-galaxy/issues/1 ).
Thank you in advance.
Mic
On Tue, Nov 17, 2015 at 9:32 AM, Eric Rasche esr@tamu.edu wrote:
That snippet is no longer needed and was fixed in 15.10.
On 11/16/2015 05:28 PM, Mic wrote:
Hi all, Thank you for your email, I found on the bottom of this site https://wiki.galaxyproject.org/Admin/Config/nginxProxy a configuration for IE, but I am not quite sure whether it is enough. To update the documentation would be really awesome.
Thank you in advance.
Mic
On Tue, Nov 17, 2015 at 12:05 AM, Björn Grüning <bjoern.gruening@gmail.com mailto:bjoern.gruening@gmail.com> wrote:
Nate configured it on Galaxy main last week, maybe I can convincehim to
update the documentation ... > Hi Mic, > > Yes... neither of us use Nginx as our primary proxy, so we never > wrote the configuration for it. > > If you use Nginx I'm assuming you're familiar with itsconfiguration.
> As you can see from the apache route, you really just need a few > proxy_pass statements. If you can write those, we'd be more than > happy to include them in our documentation. > > Ciao, Eric > > > On 11/16/2015 07:44 AM, Mic wrote: >> Hi all, Looking at this link >> (http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html )
>> >> it seem Nginx configuration is missing. >> >> How to configure Nginx for IE and Galaxy 15.10? >> >> Thank you in advance. >> >> Mic >> >> On Thu, Nov 12, 2015 at 2:36 AM, Eric Rasche <esr@tamu.edu <mailto:esr@tamu.edu> >> <mailto:esr@tamu.edu <mailto:esr@tamu.edu>>> wrote: >> >> Hi Mic, >> >> Replying off list as this seems to be a different set of issues >> than others experience. >> >> 1) From your earlier mails it sounded like you had been reading >> the docs on GIEs, but you asked for then here. Have you read >> through >>http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html
>> >> yet? If so, how far did you get? >> >> 2) do you have docker installed? what version? ("docker -v" I >> believe) >> >> 3) What release of Galaxy are you on? The instructions are version >> specific in places. >> >> 3) All of the files for GIEs are in >> config/plugins/interactive_environments. Have you made any changes >> to your local ipython.ini or rstudio.ini? >> >> Any logs from GIEs will appear in your normal Galaxy logs. E.g. >> paster.log >> >> Ciao, Eric >> >> 11. nov. 2015 10.05 a.m. skrev Mic <mictadlo@gmail.com <mailto:mictadlo@gmail.com> >> <mailto:mictadlo@gmail.com <mailto:mictadlo@gmail.com>>>: >> >> 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 <mictadlo@gmail.com <mailto:mictadlo@gmail.com> >> <mailto:mictadlo@gmail.com <mailto:mictadlo@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.gruening@gmail.com <mailto:bjoern.gruening@gmail.com> <mailto:bjoern.gruening@gmail.com <mailto:bjoern.gruening@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 >> <esr@tamu.edu <mailto:esr@tamu.edu> <mailto:esr@tamu.edu <mailto: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> >> <http://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 <tel:404-692-2048> >>>> <tel:404-692-2048 <tel:404-692-2048>> esr@tamu.edu <mailto:esr@tamu.edu> <mailto:esr@tamu.edu <mailto:esr@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/ >>> >> >> >> >> >-- 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