IUC Contribution Fest - RADSeq Tools and Workflows

[tiagoantao]

We are planning a Remote Contribution Fest on 7th and 8th of March for developers to work on Galaxy RADSeq tools.

RADSeq is a cheap sequencing technology that is used by many resource-limited groups who would benefit a lot from easy-to-use galaxy tools. Indeed there has been quite some interest in analyzing RADSeq with Galaxy. Currently there is a wrapper for stacks and little more to help with RAD specific analysis (though many other galaxy tools are useful with RADs - bwa, cap3, gatk, velvet, ...).

If you are interested in participating in the hackathon but not interested in actual tool development - we will assemble a list of smaller, manageable Python and JavaScript tasks to work on and certainly documentation is a chronically lacking for collections so we could use help there and no actual coding would be required.

We encourage ideas or advice about how to organize this so please let us know. A core group will be available on IRC all day and we will have google hangouts across those days to organize, answer questions, and report progress.

We will do our best to coordinate and make this hackathon a nice and productive experience and we would like to especially focus on working reasonable hours and discourage overnighters.

All forms of contribution are welcome!

Google hangout link for the hackathon: https://hangouts.google.com/call/iiksaostt5dwfms4lph6nuj74ye

Original idea from @bgruening (galaxyproject/tools-devteam#26 (comment)). See #299 and #239 for information on the last two hackathons. This text is inspired on #299.

Things to work on

This list will be updated as comments are made on the issue. Your are strongly encouraged to leave your suggestion/opinion/criticism below.

Note that while the list is currently stacks-oriented, there is no reason for that to be the final list of stuff to do... Non-stacks based suggestions are strongly encouraged

• Existing stacks plugin (https://github.com/genouest/galaxy-tools/tree/master/tools/stacks)
  • Support for data collections
  • cap3 integration
  • support multi-threading (GALAXY_SLOTS)
  • upgrade the version of stacks
  • support clone_filter
• Implement stacks workflows
• Check the feasibility of implementing the stacks web interface on Galaxy
• have a process_radtags alike with a configurable enzyme sequence (i.e allow demultiplexing using a configurable sequence)
• PyRAD
• dDocent

  Reading list

• Stacks homepage
• Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags
• Analyse de données RADseq sous Galaxy : l'exemple de STACKS - In French from @yvanlebras
• PyRAD documentation - Jupyter notebook

[tiagoantao]

@mvdbeek would you think it would make sense to have a bioconda version of cap3?

[tiagoantao]

@mvdbeek Please ignore my idea, cap3 seems to have a non-free license. I will be using your packages directly and not worry with bioconda

[mvdbeek]

There is a script called exec_velvet.pl in stacks that uses velvet. We would like it to use cap3. There is probably no need to make a new tool (evaluating that), just integrating them.

okay I see!

Please ignore my idea, cap3 seems to have a non-free license. I will be using your packages directly and not worry with bioconda

Ah, yes, we'll need to display that license on our package :/

[tiagoantao]

@yvanlebras Another PR for stacks can be found here: https://github.com/genouest/galaxy-tools/pull/4

[yvanlebras]

Thanks! We will hangout this afternoon....

Envoyé depuis mon appareil Samsung

-------- Message d'origine -------- De : Tiago Antao notifications@github.com Date : 07/03/2016 11:46 (GMT+01:00) À : galaxyproject/tools-iuc tools-iuc@noreply.github.com Cc : yvanlebras yvan.le_bras@irisa.fr Objet : Re: [tools-iuc] IUC Contribution Fest - RADSeq Tools and Workflows (#422)

@yvanlebras Another PR for stacks can be found here: genouest/galaxy-tools#4

— Reply to this email directly or view it on GitHub.

[tiagoantao]

I just merged stacks support in bioconda

[bgruening]

@tiagoantao awesome! I'm now in and try to review PR :)

[bgruening]

@tiagoantao we are now in the hangout. Also here is a Trello board: https://trello.com/b/EfGYBOPX/hackthon-radseq

[tiagoantao]

@yvanlebras / @bgruening Question: the current correct place to work on the stacks tool is: https://github.com/galaxyproject/tools-iuc/tree/stacks Not the old: https://github.com/genouest/galaxy-tools correct?

I am going to work on cap3 on whatever repo you tell me to...

[abretaud]

Yes that's it, no more work on genouest github now

[tiagoantao]

@abretaud thanks!

[yvanlebras]

Is it a way @jpuritz to help us implementing dDocent ? If we well understood, the user normally have to follow "the text based prompts". Which way you think is the best to integrate dDocent in Galaxy ?

I'm thinking about the fact to use an Interactive Environment to deploy dDocent on a Docker, interactively choose the parameters using "the text based prompts" then export something like a config file we can use as an input to a Galaxy dDocent tools...... Maybe it's totally out of scope....

[bgruening]

@yvanlebras here is a Docker pyrad container. Automatically created with conda packages. docker run -it --rm quay.io/mulled/pyrad:3.0.64--py27_0

https://mulled.github.io/

[yvanlebras]

Sorry Eduardo, I miss your e-mail...  As the introduction speechs were in french, hangout was not used but presentation slides are here: https://cesgo.genouest.org/tags/galhackradfr Wishing you a good day. Yvan

[bgruening]

@yvanlebras what do you mean here?

[yvanlebras]

@bgruening concerning our presentations of tomorrow morning ? We made it in French, so we have not used hangout to avoid proposing "english speaking" colleagues to hear us speaking french.....

[bgruening]

Uh, I was referring to an other comment of you that disappeared. Never mind. We should all learn Esperanto ;)

[yvanlebras]

+1 ;) or deutsch !

[Eduardo-Alves]

I speak french! But its' ok, I had the slides so I read them instead of the hangout.

Eduardo

On Tue, Mar 8, 2016 at 1:35 PM, Björn Grüning notifications@github.com wrote:

Uh, I was referring to an other comment of you that disappeared. Never mind. We should all learn Esperanto ;)

— Reply to this email directly or view it on GitHub https://github.com/galaxyproject/tools-iuc/issues/422#issuecomment-193786814 .

[tiagoantao]

@yvanlebras et al: Are you planning to add any test data snippet to the stacks tool? For automated testing purposes.

If you have something to test STACKS_sort_read_pairs , I could re-use it with my version without velvet...

[tiagoantao]

Sorry, closed by mistake...

[yvanlebras]

Yes, for sure! For sort_read_pairs, you can use the original STACKS sample data : http://catchenlab.life.illinois.edu/stacks/pe_tutorial/pe_samples.tar.gz

[yvanlebras]

For other STACKS scripts, I propose some datasets here

[tiagoantao]

@yvanlebras thanks!

[tiagoantao]

@yvanlebras Just one thing: we might have to add some of these to the tool in order to have automated testing...

[yvanlebras]

@tiagoantao Yes, of course! ;) we are adding data for each tools to enable functional testing...

[bgruening]

@tiagoantao we are on it in the latest PR. The problem is that we encountered a few planemo/tools issues we need to sort out. But we are working on it.

[yvanlebras]

In France, we don't have anything to eat now... so we must stop here for the day!

A preliminary report of our participation: http://cesgo.genouest.org/groups/guggo/wiki/RADseqHackathon

Don't hesitatre to comment / react !

Whishing you a good end of day!

[bgruening]

Thanks a lot @yvanlebras + team! Keep the PR coming!

[tiagoantao]

When do you guys think the new stacks version will hit the toolshed? Selfish-me here talking, I would like to install it ASAP. ;)

I am finalizing the sort_pair_reads / velvet decoupling, but that can go later...

[abretaud]

There is quite some work left to do, personally I will continue to work on this in the coming weeks, but after a week of holidays ;)

[lecorguille]

@yvanlebras https://github.com/yvanlebras The dataset, you produce for ref_map, is a little poor. I get empty tsv ( https://github.com/galaxyproject/tools-iuc/tree/stacks/tools/stacks/test-data). Or perhaps I'm to strong in my parameters (population with -n 3 -m 1)

2016-03-09 9:20 GMT+01:00 Anthony Bretaudeau notifications@github.com:

There is quite some work left to do, personally I will continue to work on this in the coming weeks, but after a week of holidays ;)

— Reply to this email directly or view it on GitHub https://github.com/galaxyproject/tools-iuc/issues/422#issuecomment-194178656 .

[yvanlebras]

This is not your parameters, only the data who are poor, you're right. If you need something who generates not empty file for this last population step, I need some additional time ;) I will try today... Thanks for pointing this!

Envoyé depuis mon appareil Samsung

-------- Message d'origine -------- De : Gildas Le Corguillé notifications@github.com Date : 09/03/2016 09:53 (GMT+01:00) À : galaxyproject/tools-iuc tools-iuc@noreply.github.com Cc : yvanlebras yvan.le_bras@irisa.fr Objet : Re: [tools-iuc] IUC Contribution Fest - RADSeq Tools and Workflows (#422)

@yvanlebras https://github.com/yvanlebras The dataset, you produce for ref_map, is a little poor. I get empty tsv ( https://github.com/galaxyproject/tools-iuc/tree/stacks/tools/stacks/test-data). Or perhaps I'm to strong in my parameters (population with -n 3 -m 1)

2016-03-09 9:20 GMT+01:00 Anthony Bretaudeau notifications@github.com:

There is quite some work left to do, personally I will continue to work on this in the coming weeks, but after a week of holidays ;)

— Reply to this email directly or view it on GitHub https://github.com/galaxyproject/tools-iuc/issues/422#issuecomment-194178656 .

---

Reply to this email directly or view it on GitHub: https://github.com/galaxyproject/tools-iuc/issues/422#issuecomment-194188437

[tiagoantao]

If it takes some time, then I will soon submit a PR with the sort_read_pairs decoupling

[martenson]

Closing this issue since this codefest is long finished. Thanks all!