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galaxyproteomics / tools-galaxyp

Galaxy Tool Shed repositories maintained and developed by the GalaxyP community
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Hackathon on conda packaging: September 27th and 28th #57

Closed bgruening closed 7 years ago

bgruening commented 8 years ago

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 commented 8 years ago

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

bgruening commented 8 years ago

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

souravsingh commented 8 years ago

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

bgruening commented 8 years ago

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

PratikDJagtap commented 7 years ago

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.

bgruening commented 7 years ago

ping @galaxyproteomics/developers!

blankenberg commented 7 years ago

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.

bgruening commented 7 years ago

@blankenberg done!

lecorguille commented 7 years ago

I'm in!

bgruening commented 7 years ago

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

iracooke commented 7 years ago

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.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

bgruening commented 7 years ago

@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 commented 7 years ago

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/

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

souravsingh commented 7 years ago

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

bgruening commented 7 years ago

@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!

PratikDJagtap commented 7 years ago

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!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/galaxyproteomics/tools-galaxyp/issues/57#issuecomment-249549591, or mute the thread https://github.com/notifications/unsubscribe-auth/AKL0OnBzIGbFTF2LPTb5kM6ZNo9k_2YUks5qt7JTgaJpZM4H93nq .

chambm commented 7 years ago

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

Does Conda build everything from source?

bgruening commented 7 years ago

@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!

bgruening commented 7 years ago

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

bgruening commented 7 years ago

Let's start the Codefest in Europe! :)

bgruening commented 7 years ago

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

bgruening commented 7 years ago

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

iracooke commented 7 years ago

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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