Re: [galaxy-dev] 20 August GalaxyAdmins Meetup: Genomic Data Management; Tool Installation Automation

[Björn Grüning]

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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Re: [galaxy-dev] 20 August GalaxyAdmins Meetup: Genomic Data Management; Tool Installation Automation

[mark fernandes (IFR)]

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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Re: [galaxy-dev] 20 August GalaxyAdmins Meetup: Genomic Data Management; Tool Installation Automation

[Dave Clements]

Hi All,

Just a reminder that the next GalaxyAdmins online meetup is tomorrow,
Thursday, August 20

 at your local time

.

It can take a few minutes to connect so you aren encouraged to start the
process a few minutes early.

Hope to see you tomorrow,

Dave C

On Thu, Aug 13, 2015 at 10:47 AM, Dave Clements 
wrote:

> Hello all,
>
> The next GalaxyAdmins online meetup is next week, on Thursday, August 20
> .
> The featured topics are:
>
>
>- *Genomic data management at Canada's National Microbiology
>Laboratory  with IRIDA
> and Galaxy*, presented by Aaron Petkau
>
>- *Adding transparency and automation into the Galaxy tool
>installation process , *presented
>by Enis Afgan 
>
> The meetup will use the same Adobe Connect technology
> 
> used on previous calls.  It takes a couple of minutes to connect, so you
> are encouraged to start connecting a few minutes early.
>
> See your local time
> 
> to know when to connect.
>
> Looking forward to our first post-GCC gathering,
>
> Dave C and Hans-Rudolf
>
> --
> http://galaxyproject.org/
> http://getgalaxy.org/
> http://usegalaxy.org/
> https://wiki.galaxyproject.org/
>



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