Re: [galaxy-dev] 20 August GalaxyAdmins Meetup: Genomic Data Management; Tool Installation Automation
Sounds like this will be an interesting meeting and quite germane to a requirement of mine. I want to achieve an environment as follows: 1) Galaxy Docker container (Thanks Bjorn :-) )with minimal tools deliverable to course developers machine e.g. via Kitematic 2) Course developer adds minimal set of Galaxy tools required to deliver course 3) Developer then adds shared data, workflows, notes & materials and tests everything. 4) Runs tools to extract tools etc to an export set 5) Course can be then deployed to a (local) Training server's Docker container using complementary set of tools to import from the export set (or to a user's desktop e.g.via Kitematic as part of an e-learning environment) Currently working my way through Bioblend API docs & notes from GCC 2015 workshop to see how much of this is achievable (also have Bjorn's notes on cloning tools from Galaxy Main which I hope to adapt). Any advice/insights welcomed along with any advances in automation from Development team. Regards, Mark Fernandes Bioinformatics/Biomathematics Training Training information blog: http://scicomp-training.ifr.ac.uk/ 'Open door' BI/BM training surgery (i.e. just turn up) every Thursday 2.30pm-3.30pm T: +44 (0)1603 255000 Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK www.ifr.ac.uk Facebook | Twitter | LinkedIn | YouTube The Institute of Food Research receives strategic funding from BBSRC
Hi Mark, please have a look at https://github.com/bgruening/galaxy-rna-workbench-extra Here we try to develop small scripts to load data into a library and setting up everything for a workshop. Indeed this container was used for a few workshops already but is still under development. The plan is to move useful tools into the main Galaxy Docker image at some point. Our goal is to deliver training material + frozen Docker containers so everyone can exactly reproduce a workshop. Hope this helps! Bjoern
Sounds like this will be an interesting meeting and quite germane to a requirement of mine.
I want to achieve an environment as follows: 1) Galaxy Docker container (Thanks Bjorn :-) )with minimal tools deliverable to course developers machine e.g. via Kitematic 2) Course developer adds minimal set of Galaxy tools required to deliver course 3) Developer then adds shared data, workflows, notes & materials and tests everything. 4) Runs tools to extract tools etc to an export set 5) Course can be then deployed to a (local) Training server's Docker container using complementary set of tools to import from the export set (or to a user's desktop e.g.via Kitematic as part of an e-learning environment)
Currently working my way through Bioblend API docs & notes from GCC 2015 workshop to see how much of this is achievable (also have Bjorn's notes on cloning tools from Galaxy Main which I hope to adapt).
Any advice/insights welcomed along with any advances in automation from Development team.
Regards, Mark Fernandes Bioinformatics/Biomathematics Training Training information blog: http://scicomp-training.ifr.ac.uk/ 'Open door' BI/BM training surgery (i.e. just turn up) every Thursday 2.30pm-3.30pm
T: +44 (0)1603 255000 Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK
www.ifr.ac.uk Facebook | Twitter | LinkedIn | YouTube
The Institute of Food Research receives strategic funding from BBSRC
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participants (2)
-
Björn Grüning -
mark fernandes (IFR)