Re: [galaxy-dev] IPython and Rstudio are missing
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> wrote:
Nate configured it on Galaxy main last week, maybe I can convince him 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 its configuration. 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>> 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>>:
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>> 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>> 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>> 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
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> --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
pkg-config liblzma-dev libbz2-dev libpcre3-dev/ /apt-get install libblas-dev liblapack-dev gfortran
/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
(and rstudio/config/rstudio.xml) files to add a line like: libc-dev pandoc libzmq3-dev curl/ 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> 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/
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 convince him 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 its configuration. > 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
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 convince him 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 its configuration. > 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
Hi all, I found the following Nginx configuration here ( https://github.com/fredhutchio/docker-galaxy/blob/master/nginx.conf ). Unfortunately, I could not start the docker container ( https://github.com/fredhutchio/docker-galaxy/issues/1 ). Thank you in advance. Mic On Thu, Dec 31, 2015 at 9:33 AM, Mic <mictadlo@gmail.com> wrote:
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 convince him 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 its configuration. > 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
Hi Mic, I'm not entirely sure what you are searching for. You already used this one right? https://github.com/bgruening/docker-galaxy-stable Docker and IPython should work here. You will find a nginx.conf included in this as well or you can use the ansible playrole here with all describtions on howto setup a Galaxy instance with nginx. https://github.com/galaxyproject/ansible-galaxy-extras Ciao, Bjoern Am 31.12.2015 um 00:37 schrieb Mic:
Hi all, I found the following Nginx configuration here ( https://github.com/fredhutchio/docker-galaxy/blob/master/nginx.conf ).
Unfortunately, I could not start the docker container ( https://github.com/fredhutchio/docker-galaxy/issues/1 ).
Thank you in advance.
Mic
On Thu, Dec 31, 2015 at 9:33 AM, Mic <mictadlo@gmail.com> wrote:
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 convince him 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 its configuration. > 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
Hi Bjoern, Yes, I try to use galaxy-docker-stable and I could not get IE running. Therefore, I have opened this issue ( https://github.com/bgruening/docker-galaxy-stable/issues/127 ). I logged in to the container and the ipython.ini and rstudio.ini are not enable: *# ls /galaxy-central/config/plugins/interactive_environments/rstudio/configrstudio.ini.sample rstudio.xmlroot@77fcf1e4b798:~# ls /galaxy-central/config/plugins/interactive_environments/ipython/configipython.ini.sample ipython.xml* What did I do wrong? Thank you in advance. Mic On Fri, Jan 1, 2016 at 10:21 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Mic,
I'm not entirely sure what you are searching for. You already used this one right?
https://github.com/bgruening/docker-galaxy-stable
Docker and IPython should work here.
You will find a nginx.conf included in this as well or you can use the ansible playrole here with all describtions on howto setup a Galaxy instance with nginx.
https://github.com/galaxyproject/ansible-galaxy-extras
Ciao, Bjoern
Am 31.12.2015 um 00:37 schrieb Mic:
Hi all, I found the following Nginx configuration here ( https://github.com/fredhutchio/docker-galaxy/blob/master/nginx.conf ).
Unfortunately, I could not start the docker container ( https://github.com/fredhutchio/docker-galaxy/issues/1 ).
Thank you in advance.
Mic
On Thu, Dec 31, 2015 at 9:33 AM, Mic <mictadlo@gmail.com> wrote:
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 convince him 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 its configuration. > 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
participants (3)
-
Björn Grüning -
Eric Rasche -
Mic