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Hackathon on conda packaging: September 27th and 28th #57

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bgruening opened this Issue Apr 1, 2016 · 23 comments

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@bgruening
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bgruening commented Apr 1, 2016

Hi GalaxyP Community,

I would like to invite you to a hackathon on the September 27th and 28th. We will package as many dependencies as possible into conda packages.

Conda is a new packaging system that Galaxy can use and that enables travis tool testing, finally! Would be great if someone can join!

We will meet tomorrow here:

https://hangouts.google.com/call/35zl5pahj5hkppxokhuxvszx24e
and on gitter here:
https://gitter.im/GalaxyProteomics/Lobby

Some slides for a Conda quick-start can be found here: https://galaxy.slides.com/bgruening/conda-quick-start/live#/

A tool list that needs help can be found here: https://docs.google.com/spreadsheets/d/1C9p_XLiLyrbMoRVKS_H582TL1I5v9FKAv2dl5VAYxjw/edit#gid=0

@iracooke

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iracooke commented Apr 2, 2016

Hi Bjoern,

Sounds very interesting. I will follow your progress but I cant spare any time next week to participate properly. I'm moving next week to a new city

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bgruening commented Apr 3, 2016

@iracooke no problem! I will work on peptide-shaker I guess as example. Have fun moving!

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souravsingh commented Jun 18, 2016

@bgruening Is the issue still open? I would like to work on it.

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bgruening commented Jun 18, 2016

@souravsingh this is awesome! The hackathon is over yes, but I can help you to get started anytime.

@PratikDJagtap

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PratikDJagtap commented Sep 9, 2016

The first Galaxy-P CONDA hackathon will be held on September 27th and 28th.
Galaxy-P and proteomics tool developers will participate in this hackathon to "CONDA-package" some of the prioritized proteomics tools within Galaxy. The hackathon will be an online event which will start
with an introduction to Galaxy structure and CONDA packaging by Bjoern Gruening. Details soon.

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bgruening commented Sep 9, 2016

@blankenberg

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blankenberg commented Sep 9, 2016

Awesome! Any thoughts about cross posting to tools-iuc? This could be a great chance for anyone that missed @bgruening's first conda intro to get looped back in. Although, I wouldn't want to hijack/detract from the Proteomics priorities.

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bgruening commented Sep 10, 2016

@blankenberg done!

@lecorguille

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lecorguille commented Sep 12, 2016

I'm in!

@bgruening bgruening changed the title from hackathon on conda packaging to Hackathon on conda packaging: September 27th and 28th Sep 25, 2016

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bgruening commented Sep 25, 2016

Just a reminder our hackathon will start in 2 days :) Looking forward to see you all.

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iracooke commented Sep 25, 2016

Hi Bjoern
I am helping in a SC course those days. If I have idle time I will try to wrap protk galaxy tools. Is there a link with a guide?

Sent from my iPhone

On 25 Sep. 2016, at 11:02 pm, Björn Grüning notifications@github.com wrote:

Just a reminder our hackathon will start in 2 days :) Looking forward to see you all.


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bgruening commented Sep 25, 2016

@iracooke !!!
There is the official documentation: http://conda.pydata.org/docs/building/recipe.html

But I think looking at an example is in most cases enough. For example this one: https://github.com/bioconda/bioconda-recipes/tree/master/recipes/pysamstats

Install minconda2: http://conda.pydata.org/miniconda.html create those two files and run: conda build /path/to/folder/

@glormph

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glormph commented Sep 26, 2016

I will be able and happy to join 28th but not 27th (EST :) ).

Do we have a packaging agenda as to which tools are prioritized?

cheers,

Jorrit Boekel
Proteomics systems developer
Lehtiö lab / NBIS
Scilifelab Stockholm, Sweden

On 25 Sep 2016, at 23:47, Björn Grüning notifications@github.com wrote:

@iracooke !!!
There is the official documentation: http://conda.pydata.org/docs/building/recipe.html

But I think looking at an example is in most cases enough. For example this one: https://github.com/bioconda/bioconda-recipes/tree/master/recipes/pysamstats

Install minconda2: http://conda.pydata.org/miniconda.html create those two files and run: conda build /path/to/folder/


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souravsingh commented Sep 26, 2016

@bgruening I would like to join in the hackathon. Do we have a list of packages requiring a conda recipe?

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bgruening commented Sep 26, 2016

@souravsingh @glormph sounds great!
We have this one: https://docs.google.com/spreadsheets/d/1C9p_XLiLyrbMoRVKS_H582TL1I5v9FKAv2dl5VAYxjw/edit#gid=0

@PratikDJagtap need to explain this to me ;)
But essentially all tools we have here in this repo!

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PratikDJagtap commented Sep 26, 2016

Hello Bjoern and Conda packaging hackathon participants,

JJ has suggested that participants focus on their own tools and
applications of interest first, then help with the general list.

Ideally, the tools with priority 1 are those that would need to be tackled
first.

Thank you everyone for the participation!

Regards,
Pratik

Pratik Jagtap,
Research Assistant Professor, and
Managing Director, Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory, 1479 Gortner Avenue,
St. Paul, MN 55108
Phone: 612-624-9275
http://cbs.umn.edu/cmsp/

On Mon, Sep 26, 2016 at 6:53 AM, Björn Grüning notifications@github.com
wrote:

@souravsingh https://github.com/souravsingh @glormph
https://github.com/glormph sounds great!
We have this one: https://docs.google.com/spreadsheets/d/1C9p_
XLiLyrbMoRVKS_H582TL1I5v9FKAv2dl5VAYxjw/edit#gid=0

@PratikDJagtap https://github.com/PratikDJagtap need to explain this to
me ;)
But essentially all tools we have here in this repo!


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chambm commented Sep 26, 2016

Where are the details for joining the hackathon? I.e. where do I go and at what time?

Does Conda build everything from source?

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bgruening commented Sep 26, 2016

@chambm I have added a link to a hangout and one to a gitter chat room. I will be there as soon as I'm awake and will give guidance. We also will have a short presentation if this is necessary!

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bgruening commented Sep 26, 2016

Added a link to quick-start slides at the top.

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bgruening commented Sep 27, 2016

Let's start the Codefest in Europe! :)

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bgruening commented Sep 27, 2016

If anyone needs help please ping us! We are here to help you :)

@lecorguille lecorguille referenced this issue Sep 29, 2016

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WIP: add percolator #2438

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bgruening commented Sep 30, 2016

This was really fun for me!!! I hope you also enjoyed it! We wrote a little summary about this hackathon and I wanted to thank you all for your amazing contributions! I think we can do this again - next time with the focus on GalaxyP tools to make use of the conda packages?

https://gist.github.com/bgruening/97b1fa16b92f5ab30b1e7c193b286432

Again, thanks a bunch for all your help!
Bjoern

@bgruening bgruening closed this Sep 30, 2016

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iracooke commented Sep 30, 2016

Fantastic work. Sorry I was not able to participate. Hopefully next time

On 30 Sep. 2016, at 4:38 pm, Björn Grüning notifications@github.com wrote:

This was really fun for me!!! I hope you also enjoyed it! We wrote a little summary about this hackathon and I wanted to thank you all for your amazing contributions! I think we can do this again - next time with the focus on GalaxyP tools to make use of the conda packages?

https://gist.github.com/bgruening/97b1fa16b92f5ab30b1e7c193b286432 https://gist.github.com/bgruening/97b1fa16b92f5ab30b1e7c193b286432
Again, thanks a bunch for all your help!
Bjoern


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