[galaxy-dev] Galaxy training contribution fest - 6-7th October
Dear training enthusiast, the Galaxy Training Network (GTN) is planning a contribution fest to consolidate our training material and improve the overall training experience in Galaxy on the 6.-7th October 2016! More information about the project can be found here: https://gist.github.com/bgruening/a54a8600c5cddca82424ad13569708c3 and a small presentation here: http://bgruening.github.io/training-material/shared/slides/project_presentation#/ This will be an online contribution fest and the fun to contribute should be priority one! There is enough to work on in all areas, from programming to fix spelling mistakes. So everyone is welcome to improve the Galaxy training material. Ciao, Bérénice and Bjoern ___ 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/
Re: [galaxy-dev] Modifying a Cloud Cluster Instance
If you have a system that works, I don't see a need to change it. But yes, it's the Galaxy install is a clone of the repo so git pull will do the trick. On Fri, Sep 16, 2016 at 9:24 AM, Lapointe, David wrote: > Yes that looks good. The git pull will work on top of the AMI (16.04)? > I don't think that I need cloudman to stop/start, just supervisorctl, > which I have been using to manage galaxy. > > Thanks > > David > > -- > David Lapointe Ph.D. > Sr. Bioinformatics Specialist > Research Technology (RT) > Tufts Technology Services (TTS) > 16 Dearborn Road > Somerville MA 02144 > > Phone: 617-627-5319 > Fax: 617-627-3667 > http://it.tufts.edu > > From: Enis Afgan > Date: Thursday, September 15, 2016 at 5:30 PM > > To: David Lapointe > Cc: "galaxy-dev@lists.galaxyproject.org" galaxyproject.org> > Subject: Re: [galaxy-dev] Modifying a Cloud Cluster Instance > > Give you seemingly have a custom deployment, a manual upgrade is probably > best. Instructions are available here: https://wiki. > galaxyproject.org/CloudMan/Services/Galaxy#Updating_Galaxy_source > > We'll get the 16.07 release done too but juding by the way things look, it > won't be until the next month. > > On Wed, Sep 14, 2016 at 11:23 AM, Lapointe, David < > david.lapoi...@tufts.edu> wrote: > >> Hi Enis, >> >> Yes I figured what I was doing wrong. Using Cloudman to restart services >> overwrote my confs. Using the CLI to manage services keeps everything in >> place, though I would like to figure out what is the optimal way to move to >> 16.07. Wait for the AMI or update? >> -- >> David Lapointe Ph.D. >> Sr. Bioinformatics Specialist >> Research Technology (RT) >> Tufts Technology Services (TTS) >> 16 Dearborn Road >> Somerville MA 02144 >> >> Phone: 617-627-5319 >> Fax: 617-627-3667 >> http://it.tufts.edu >> >> From: Enis Afgan >> Date: Wednesday, September 14, 2016 at 11:01 AM >> To: David Lapointe >> Cc: "galaxy-dev@lists.galaxyproject.org" > t.org> >> Subject: Re: [galaxy-dev] Modifying a Cloud Cluster Instance >> >> Hi David, >> I totally missed this email from you - apologies! Are you still trying to >> do this or did you figure it out? Following the general guidelines on >> customizing the instance is a good place to start. There is an option in >> CloudMan to turn on non-signed SSL (from the Admin page) but the steps >> performed may be useful in trying to do the same manually. I believe it's >> necessary to just update and reload the Nginx configuration. A template can >> be found here https://github.com/galaxyproject/cloudman/blob/8db478a8 >> d777bcc48ed8c838f1f9de8519a11e60/cm/conftemplates/nginx_ >> server_ssl.default >> >> Hope this helps and, again, sorry for not getting back to you earlier. >> >> >> On Thu, Aug 11, 2016 at 2:30 PM, Lapointe, David < >> david.lapoi...@tufts.edu> wrote: >> >>> This is on Amazon I should add. >>> -- >>> David Lapointe Ph.D. >>> Sr. Bioinformatics Specialist >>> Research Technology (RT) >>> Tufts Technology Services (TTS) >>> 16 Dearborn Road >>> Somerville MA 02144 >>> >>> Phone: 617-627-5319 >>> Fax: 617-627-3667 >>> http://it.tufts.edu >>> >>> From: galaxy-dev on behalf >>> of David Lapointe >>> Date: Thursday, August 11, 2016 at 1:44 PM >>> To: "galaxy-dev@lists.galaxyproject.org" >> t.org> >>> Subject: [galaxy-dev] Modifying a Cloud Cluster Instance >>> >>> I have a Cloudman instance up and running, but I would like to add SSL >>> ( I have a signed cert and key ) and productionize it. I see several >>> methods documented,but it's not clear which one is preferred: edit in place >>> then persist changes and restart (wiki/Cloudman/CustomizeGalaxyCloud) >>> seems best to me. Any advice? >>> >>> Thanks >>> >>> David >>> -- >>> David Lapointe Ph.D. >>> Sr. Bioinformatics Specialist >>> Research Technology (RT) >>> Tufts Technology Services (TTS) >>> 16 Dearborn Road >>> Somerville MA 02144 >>> >>> Phone: 617-627-5319 >>> Fax: 617-627-3667 >>> http://it.tufts.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/ >>> >> >> > > > - Upozorenje - > > Automatskom detekcijom utvrdjeno je da tekst ove poruke > podsjeca na tzv. phishing poruku. > > AKO SE U PORUCI TRAZI DA POSALJETE VASU IRB LOZINKU ILI > DA UNESETE IRB PODATKE NA NAVEDENOM LINKU, RADI SE O > NAPADU S CILJEM KRADJE I ZLOUPOTREBE PODATAKA. > > Centar za informatiku i racunarstvo, > Institut Rudjer Boskovic > > - Upozorenje - > ___ Please keep all replies on the list by using "reply all" in your mail client. To ma
Re: [galaxy-dev] [galaxy-iuc] GMAP tool_dependencies.xml package for ToolShed
I would greatly appreciate the IUC adopting all gmap/gsnap work that I originally worked on. I do not currently have the time to maintain these tools. Administrative access granted to IUC for: https://toolshed.g2.bx.psu.edu/view/jjohnson/gmap/ https://toolshed.g2.bx.psu.edu/view/jjohnson/package_gmap_2013_05_09/ https://testtoolshed.g2.bx.psu.edu/view/jjohnson/gmap/ https://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_gmap_2013_05_09/ These can be copied to the iuc owned repositories and I could deprecate those under my name. On 9/20/16 8:13 AM, Peter Cock wrote: Thanks JJ :) Could you explicitly confirm that we (the IUC) have your permission to adopt the gmap wrappers and packages (and any of your other Galaxy work you might want to suggest), to develop and maintain under the IUC banner, under the MIT license. (Ideally I'd suggest you state this in an email CC'ing the galaxy-dev list as a public record) For now this will mean tracking their development in: https://github.com/galaxyproject/tools-iuc Secondly, would you be willing to grant admin/write access to the IUC account on the (main and test) tool shed for these: https://toolshed.g2.bx.psu.edu/view/jjohnson/gmap/ https://toolshed.g2.bx.psu.edu/view/jjohnson/package_gmap_2013_05_09/ Thanks, Peter On Tue, Sep 20, 2016 at 12:47 PM, Jim Johnson wrote: It would be great to move this to IUC. I originally put a lot of effort into this for a researcher at MN; I think it was tried once. I now use gmap as part a dependency of the deFuse application. Thanks, JJ -- James E. Johnson Minnesota Supercomputing Institute University of Minnesota ___ 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/
Re: [galaxy-dev] [galaxy-iuc] GMAP tool_dependencies.xml package for ToolShed
Thanks JJ, That's great. We're hoping to use GMAP locally, so I have an incentive to tackle this and the dependency glitch with the current versions on the Tool Shed. Cheers, Peter On Tue, Sep 20, 2016 at 2:50 PM, Jim Johnson wrote: > I would greatly appreciate the IUC adopting all gmap/gsnap work that I > originally worked on. > I do not currently have the time to maintain these tools. > > Administrative access granted to IUC for: > > https://toolshed.g2.bx.psu.edu/view/jjohnson/gmap/ > > https://toolshed.g2.bx.psu.edu/view/jjohnson/package_gmap_2013_05_09/ > https://testtoolshed.g2.bx.psu.edu/view/jjohnson/gmap/ > > https://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_gmap_2013_05_09/ > > These can be copied to the iuc owned repositories and I could deprecate > those under my name. > > > > On 9/20/16 8:13 AM, Peter Cock wrote: >> >> Thanks JJ :) >> >> Could you explicitly confirm that we (the IUC) have your permission >> to adopt the gmap wrappers and packages (and any of your other >> Galaxy work you might want to suggest), to develop and maintain >> under the IUC banner, under the MIT license. >> >> (Ideally I'd suggest you state this in an email CC'ing the galaxy-dev >> list as a public record) >> >> For now this will mean tracking their development in: >> https://github.com/galaxyproject/tools-iuc >> >> Secondly, would you be willing to grant admin/write access >> to the IUC account on the (main and test) tool shed for these: >> >> https://toolshed.g2.bx.psu.edu/view/jjohnson/gmap/ >> https://toolshed.g2.bx.psu.edu/view/jjohnson/package_gmap_2013_05_09/ >> >> Thanks, >> >> Peter >> >> On Tue, Sep 20, 2016 at 12:47 PM, Jim Johnson wrote: >>> >>> It would be great to move this to IUC. >>> I originally put a lot of effort into this for a researcher at MN; I >>> think >>> it was tried once. >>> I now use gmap as part a dependency of the deFuse application. >>> Thanks, >>> JJ > > > > -- > James E. Johnson Minnesota Supercomputing Institute University of Minnesota ___ 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/
