IUC Contribution Fest - Vegan, Vsearch, BIOM, Finch

galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission

https://galaxyproject.org/iuc

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IUC Contribution Fest - Vegan, Vsearch, BIOM, Finch #432

Closed nekrut closed 8 years ago

nekrut commented 8 years ago

We'll try to work out the following pipeline

load very large number of datasets (figure out upload problems @martenson )
run Kraken (explore Kraken2 @nekrut ) https://github.com/galaxyproject/tools-devteam/pull/297
test diamond (@nekrut)
reduce Kraken datasets to a single tab-delimited file (@blankenberg)
run Vegan
run VSearch
write a converter for Galaxy Taxonomy to BIOM 1.0 (@davebx)
explore Finch for viz (@davebx)
explore standalone options for Unifrac beta diversity (http://pycogent.org/ --> http://pycogent.org/cookbook/community_analysis.html#unifrac is used by QIIME/ defunct? FastUnifrac) (@blankenberg)

bgruening commented 8 years ago

Awesome! @bebatut are you working currently on Diamond?

bebatut commented 8 years ago

@bgruening I'm tested the PR #428

bgruening commented 8 years ago

@bebatut please comment on it. If you think it's good or bad :) Thanks!

blankenberg commented 8 years ago

reduce Kraken datasets to a single tab-delimited file (@blankenberg)
- Collections join on tabular columns: https://github.com/galaxyproject/tools-iuc/pull/434
- Cut tool to accept stepsize in ranges: https://github.com/galaxyproject/galaxy/pull/1190

blankenberg commented 8 years ago

Fix for PEAR: https://github.com/galaxyproject/tools-iuc/pull/438

nekrut commented 8 years ago

Added tests for Kraken https://github.com/galaxyproject/tools-devteam/pull/297

jxtx commented 8 years ago

For converting to BIOM, would it make sense to go directly from Kraken output? It looks like this would be a relatively simple modification to kraken-report. A --biom option has been requested multiple times on their mailing list so this would be a valuable upstream contribution rather than just good for Galaxy. Would require somebody to hack some Perl however.

nekrut commented 8 years ago

@jxtx: yep, this is what @davebx is currently working on

nekrut commented 8 years ago

It appears diamond will have to wait: it cannot format standard nr database from ncbi https://github.com/bbuchfink/diamond/issues/25

bgruening commented 8 years ago

@nekrut Looking in my old histories I think the old version of diamond and the data manager was working for me on NR. I hope he can fix it.

nekrut commented 8 years ago

looks like it cannot tolerate dashes. This should not be happening in nr, but who knows. Editing nr is really out of question I think.

nekrut commented 8 years ago

Also, it appears that Diamond is virtually dead - there is no active development there

bgruening commented 8 years ago

@nekrut still interested in Diamond?

peterjc commented 8 years ago

Diamond lives! :)

v0.7.10 was just released - see GitHub https://github.com/bbuchfink/diamond/ - including a fix for the strange minus signs in protein sequences (treats them as X).

bgruening commented 8 years ago

@peterjc https://github.com/galaxyproject/tools-iuc/pull/465 :)

nekrut commented 8 years ago

cool. I'll finish it

bgruening commented 8 years ago

@nekrut I have updated VSearch and put it under automatic travis testing. Phinch in also now part of Galaxy-dev (thanks to @shiltemann). Moreover, I added Vegan and Phinch to the metagenomic-flavour.

Please feel free to check those off and let us know where we can help.