galaxy-dev December 2015

galaxy-dev@lists.galaxyproject.org

41 participants
59 discussions

Re: [galaxy-dev] IPython and Rstudio are missing
by Mic 01 Jan '16

01 Jan '16

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(a)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(a)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(a)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(a)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(a)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(a)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> --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> esr(a)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/ > >>> > >> > >> > >> > >> > > >

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Tool Release Announcement: JBrowse-in-Galaxy v0.4
by Eric Rasche 31 Dec '15

31 Dec '15

Howdy Galaxy devs, A quick tool release announcement to ring in the new year. The latest version of the JBrowse-in-Galaxy tool is now available! https://toolshed.g2.bx.psu.edu/view/iuc/jbrowse/7342f467507b This tool was discussed in a lightning talk at GCC2015 but would not install nicely due to a broken dependency chain. This has since been fixed and many features added in the latest version: * Support for dataset collections * Support for multiple contigs/genomes within the JBrowse instance * Excessive configuration options for controlling colouring of tracks * Removed interstitial, open JBrowse in the main panel with one click. * Support for translation tables other than table 1. More details in the pull request <https://github.com/galaxyproject/tools-iuc/pull/507> for the curious. And a silly image to top it off :) Ciao, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu

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Re: [galaxy-dev] IE setup problem
by Mic 28 Dec '15

28 Dec '15

Hi Eric, Thank you for your email. I have Galaxy installed in */home/galaxy/galaxy* and Apache Proxy is setup for *localhost:8080*. I modified the Apache config file further for GIE: *RewriteEngine onRewriteRule ^/static/style/(.*) /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]RewriteRule ^/static/scripts/(.*) /home/galaxy/galaxy/static/scripts/packed/$1 [L]RewriteRule ^/static/(.*) /home/galaxy/galaxy/static/$1 [L]RewriteRule ^/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L]RewriteRule ^/robots.txt /home/galaxy/galaxy/static/robots.txt [L]RewriteRule ^(.*) http://localhost:8080$1 [P]# IPython specific. Other IEs may require their own routes.ProxyPass /gie_proxy/ipython/api/kernels ws://localhost:8800/gie_proxy/ipython/api/kernels# Global GIE configurationProxyPass /gie_proxy http://localhost:8800/gie_proxy <http://localhost:8800/gie_proxy>ProxyPassReverse /gie_proxy http://localhost:8800/gie_proxy <http://localhost:8800/gie_proxy># Normal Galaxy configurationProxyPass / http://localhost:8080 <http://localhost:8080>ProxyPassReverse / http://localhost:8080 <http://localhost:8080>* Did I modify the above files correctly? *Thank you in advance,* *Mic* On Tue, Dec 22, 2015 at 4:15 AM, Eric Rasche <esr(a)tamu.edu> wrote: > I'll look at this tonight, if no one else replies earlier today. Sorry to > hear you're having these troubles Mic. GIEs can be tough to deploy. Thanks > for bearing with us. > > Cheers, > Eric > > 2015-12-20 20:57 GMT-06:00 Mic <mictadlo(a)gmail.com>: > >> Hi all, >> I tried with *dynamic_proxy_manage=True* and *dynamic_proxy_manage=False*, >> but IE does not start inside Galaxy on a Annovar tab separated file (see >> attached). >> >> I also tried the following commands, but without any luck: >> >> $ node /home/galaxy/galaxy/lib/galaxy/web/proxy/js/lib/main.js --ip >> 0.0.0.0 --port 8800 --sessions >> /home/galaxy/galaxy/database/session_map.sqlite --cookie galaxysession >> --verbose >> Watching path /home/galaxy/galaxy/database/session_map.sqlite >> Listening on 0.0.0.0:8800 >> >> $ node /home/galaxy/galaxy/lib/galaxy/web/proxy/js/lib/main.js --ip >> 127.0.0.1 --port 8800 --sessions >> /home/galaxy/galaxy/database/session_map.sqlite --cookie galaxysession >> --verbose >> Watching path /home/galaxy/galaxy/database/session_map.sqlite >> Listening on 127.0.0.1:8800 >> >> $ node /home/galaxy/galaxy/lib/galaxy/web/proxy/js/lib/main.js --ip >> localhost --port 8800 --sessions >> /home/galaxy/galaxy/database/session_map.sqlite --cookie galaxysession >> --verbose >> Watching path /home/galaxy/galaxy/database/session_map.sqlite >> Listening on localhost:8800 >> >> My Galaxy is running on *0.0.0.0:8080 <http://0.0.0.0:8080>* view at *http://127.0.0.1:8080 >> <http://127.0.0.1:8080>*. I use Docker version 1.9.1, build a34a1d5. >> >> Please find attached my *galaxy.ini* and apache proxy config file ( >> *000-default.conf*). >> >> The following Apache modules I have enabled (*sudo a2enmod rewrite >> deflate expires proxy proxy_html xsendfile xml2enc proxy_wstunnel*) >> >> What did I do wrong so I can not start Rstudio and IPython inside Galaxy? >> >> Thank you in advance. >> >> Mic >> >> >> >> >> On Sat, Dec 19, 2015 at 1:12 PM, John Chilton <jmchilton(a)gmail.com> >> wrote: >> >>> dynamic_proxy_manage_proxy=True is a terrible hack, I would set it to >>> False and use supervisord if you have any inclination to at all. Like >>> sqlite or the local job runner, it is just an attempt to make sure >>> things work out of the box but it isn't that robust. >>> >>> -John >>> >>> On Sat, Dec 19, 2015 at 1:20 AM, Eric Rasche <esr(a)tamu.edu> wrote: >>> > >>> > 19. des. 2015 1.17 a.m. skrev "Mic" <mictadlo(a)gmail.com>: >>> >> >>> >> Hi all, >>> >> Thank you for the responses. If I would use >>> >> "dynamic_proxy_manage_proxy=True" than Galaxy would execute >>> automatically: >>> >> >>> >> /lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ >>> >> --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ >>> >> --cookie galaxysession --verbose >>> >> >>> >> without the need to use supervisors config? >>> > >>> > Yes. That's the idea. I'm not sure I trust it quite as much as >>> supervisord, >>> > but it has worked quite well for us so far :-) >>> > >>> >> >>> >> Thank you in advance. >>> >> >>> >> Mic >>> >> >>> >> >>> >> >>> >> On Sat, Dec 19, 2015 at 12:26 AM, Eric Rasche <esr(a)tamu.edu> wrote: >>> >>> >>> >>> Hi Mic, >>> >>> >>> >>> Since you asked for the supervisord config... it would look something >>> >>> like this:] >>> >>> >>> >>> [program:galaxy_proxy] >>> >>> command=/usr/local/bin/node >>> >>> /path/to/galaxy/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 --port >>> 8800 >>> >>> --sessions /path/to/galaxy/database/session_map.sqlite --cookie >>> >>> galaxysession --verbose >>> >>> numprocs=1 >>> >>> autostart=true >>> >>> autorestart=true >>> >>> startsecs=10 >>> >>> user=galaxy-user >>> >>> directory=/galaxy/home/directory >>> >>> umask=022 >>> >>> >>> >>> >>> >>> Galaxy can also automatically manage the proxy for you, if you set >>> >>> "dynamic_proxy_manage_proxy=True" in your galaxy.ini >>> >>> >>> >>> On 12/18/2015 01:23 AM, Björn Grüning wrote: >>> >>> > Hi, >>> >>> > >>> >>> > you need to have node installed. >>> >>> > >>> >>> > And then simply run: ./lib/galaxy/web/proxy/js/main.js --ip >>> 0.0.0.0 \ >>> >>> > --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ >>> >>> > --cookie galaxysession --verbose >>> >>> > >>> >>> > from your Galaxy root dir. >>> >>> > >>> >>> > Cheers, >>> >>> > Bjoern >>> >>> > >>> >>> > Am 18.12.2015 um 06:58 schrieb Mic: >>> >>> >> Hello, >>> >>> >> I am using the latest stable Galaxy with PostgreSQL and Apache >>> Proxy. >>> >>> >> I am >>> >>> >> trying to follow this instruction >>> >>> >> >>> >>> >> >>> http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html >>> >>> >> in order to be able to setup IE (Rstudio and Ipython). However, >>> I do >>> >>> >> not >>> >>> >> know how to setup automatically Supervisord for this command: >>> >>> >> >>> >>> >> node $GALAXY_ROOT/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ >>> >>> >> --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ >>> >>> >> --cookie galaxysession --verbose >>> >>> >> >>> >>> >> 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/ >>> >>> >> >>> >>> > ___________________________________________________________ >>> >>> > 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(a)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(a)tamu.edu >

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IE setup problem
by Mic 20 Dec '15

20 Dec '15

Hello, I am using the latest stable Galaxy with PostgreSQL and Apache Proxy. I am trying to follow this instruction http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html in order to be able to setup IE (Rstudio and Ipython). However, I do not know how to setup automatically Supervisord for this command: node $GALAXY_ROOT/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose Thank you in advance Mic

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This job is waiting to run - Issue after Update to 15.10
by Matthias Enders 20 Dec '15

20 Dec '15

Dear Galaxy Community, after updating my Galaxy instance to 15.10 via Git, I encountered a strange "This job is waiting to run" issue. When starting a new job, (even reloading a successfull one) the result dataset remains in the status "This job is waiting to run" The NCBI Blast+ tools as well as the chart tools (Boxplot, Barplot and so on) are not affected. Wheras all other tools are, including Filter, Sort and the other Build in tools as well as our own developed tools. A reload of the tool config via the admin console was successfull but did´t solve the problem. Can you give me a hint how to solve this? I´m using a Ubuntu 14.04 Server, if this is of interest. Many thanks in advance!

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How does one run Javascript or HTML as a tool?
by rbrown1422＠comcast.net 19 Dec '15

19 Dec '15

Good evening Galaxy team, Is it possible to run JavaScript or HTML as a tool or a display module? I see support for URLs, e.g. UCSC Genome Browser, but I would like to process a specific datatype to allow it to be viewed in Galaxy -- but the application is a combination of HTML and JavaScript. Does Galaxy support this? Thank you, Bob

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IE Apache Proxy config file
by Mic 19 Dec '15

19 Dec '15

Hello, I would like to setup Rstudio and IPython using Apache Proxy. I found the following settings: # IPython specific. Other IEs may require their own routes.ProxyPass /galaxy/gie_proxy/ipython/api/kernels ws://localhost:8800/galaxy/gie_proxy/ipython/api/kernels # Global GIE configurationProxyPass /galaxy/gie_proxy http://localhost:8800/galaxy/gie_proxyProxyPassReverse /galaxy/gie_proxy http://localhost:8800/galaxy/gie_proxy # Normal Galaxy configurationProxyPass /galaxy http://localhost:8000/galaxyProxyPassReverse /galaxy http://localhost:8000/galaxy However, I am not sure where to insert them and does the above settings include also Rstudio? Could anyone post their Apache Proxy settings? Thank you in advance. Mic

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INIT script for Ubuntu
by Mic 19 Dec '15

19 Dec '15

Hello, Where could I find INIT script for Ubuntu (14.04) and how to set is up? Thank you in advance. Mic

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Rstudio and Ipython supported versions for IE
by Mic 19 Dec '15

19 Dec '15

Hello, Which Rstudio and Jupyter/ipython versions are supported by IE? Thank you in advance. Mic

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GCC2016 Web Site is Up: Including registration rates, and full training schedule
by Dave Clements 18 Dec '15

18 Dec '15

Hello all, We are pleased to announce that the *2016 Galaxy Community Conference website is now online <http://gcc2016.iu.edu/>* and includes registration information <http://gcc2016.iu.edu/registration/index.php> and the full training schedule <https://gcc16.sched.org/grid-full#2016-06-26>. GCC2016 <http://gcc2016.iu.edu/> will be held June 25-29 at Indiana University <http://indiana.edu/> in Bloomington, Indiana, United States. This will be the 7th annual gathering of the Galaxy community, and we are expecting over 200 participants again this year. Registration information <http://gcc2016.iu.edu/registration/index.php> includes the different registration packages, rates, and deadlines. Our inexpensive early registration rates start at less than $40 per day for students and post-docs. Registration will open within a month. The training schedule <https://gcc16.sched.org/grid-full#2016-06-26> includes session descriptions, prerequisites, and instructors. Many thanks to everyone who nominated and voted on topics, and especially to the many instructors <https://gcc16.sched.org/directory/artists> who are contributing their time and effort to make GCC2016 a success. Thanks also go to the Indiana University Pervasive Technology Institute (PTI) <https://pti.iu.edu/>, who are supporting GCC2016 as a *Platinum Sponsor <https://gcc2016.iu.edu/sponsors/index.php>*. PTI is home to the National Center for Genome Analysis Support <http://ncgas.org/> (for which NSF funding was recently renewed <https://itnews.iu.edu/articles/2015/iu-genome-analysis-center-wins-national…>), and the Galaxy Trinity instance <https://galaxy.ncgas-trinity.indiana.edu/root>, and is a long time supporter of the Galaxy Community. PTI pairs fundamental academic computational research with the widely known strengths of Indiana University through innovations and service delivery in networking and high performance computing. See the PTI website <http://pti.iu.edu/> for more information. We continue to seek other sponsors as well and offer a wide range of sponsorship plans <https://gcc2016.iu.edu/sponsors/index.php>. If your organization is interested in having a presence at GCC2016, please contact the GCC2016 Exec <gcc2016-exec(a)lists.galaxyproject.org> for more information. Hope to see you in Bloomington! The GCC2016 Exec <gcc2016-exec(a)lists.galaxyproject.org> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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galaxy-dev December 2015