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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
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Tools request - chloroplast and mitochondrial assemblies #3392

Open dougsd3 opened 3 years ago

dougsd3 commented 3 years ago

One thing thet really called my attention was the lack or chloroplast/mitochondrial assembly tools in Galaxy. Recently, Novoplasty was included, but I feel others could be added.

I would recommend:

1- Getorganelle: https://github.com/Kinggerm/GetOrganelle (assembles chloroplast and mitochondria) 2- Organelle_PBA: https://github.com/aubombarely/Organelle_PBA (devoted to PacBio reads) 3- Chloro: https://github.com/sestaton/Chloro (an abandoned project who might be adopted by Galaxy) 4- MITObin (devoted for mitochondria, but I've heard it works well with chloroplasts): https://github.com/chrishah/MITObim https://github.com/galaxyproject/tools-iuc/pull/3400 4- OGA (Organelle Genome assembler): https://github.com/quxiaojian/OGA

These requests are quite in order of priority I would recommend.

best regards Douglas

bernt-matthias commented 3 years ago

Is there an order in the list? Do you have any favorites?

bernt-matthias commented 3 years ago

Could you check which are allready on bioconda?

dougsd3 commented 3 years ago

I put them pretty much in the order.

I'll if they're available at bioconda.

Thanks Douglas

Em dom, 20 de dez de 2020 13:47, M Bernt notifications@github.com escreveu:

Is there an order in the list? Do you have any favorites?

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dougsd3 commented 3 years ago

Getorganelle is the only one avaliable in bioconda, but it is the most up-to-date one. I would strongly recommend going further with it, because it fits to mitochondrial and chloroplast genomes

dougsd3 commented 3 years ago

https://bioconda.github.io/recipes/getorganelle/README.html

bernt-matthias commented 3 years ago

@dougsd3 even if not your favourite you may want to have a look here https://github.com/galaxyproject/tools-iuc/pull/3400 .. comments welcome.

For GetOrganelle some changes might be necessary https://github.com/Kinggerm/GetOrganelle/issues/64

bernt-matthias commented 3 years ago

Maybe the list should be extended by

Already available

dougsd3 commented 3 years ago

that's good -- Douglas Silva Domingues, PhD Research Professor Group of Genomics and Transcriptomes in Plants Institute of Biosciences at Rio Claro UNESP - Sao Paulo State University Av. 24-A, 1515 - Botany Building 13506-900, Rio Claro, SP, Brazil Phone: +55 19 35264207 e-mail: doug@rc.unesp.br GoogleScholar: http://tinyurl.com/dougpublications https://tinyurl.com/dougpublications

Em ter., 29 de dez. de 2020 às 17:07, M Bernt notifications@github.com escreveu:

@dougsd3 https://github.com/dougsd3 even if not your favourite you may want to have a look here #3400 https://github.com/galaxyproject/tools-iuc/pull/3400 .. comments welcome.

For GetOrganelle some changes might be necessary Kinggerm/GetOrganelle#64 https://github.com/Kinggerm/GetOrganelle/issues/64

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stephanflemming commented 3 years ago

An update for plasmidSPAdes is part of this PR https://github.com/galaxyproject/tools-iuc/pull/2612

bernt-matthias commented 3 years ago

https://github.com/pedronachtigall/MITGARD

dougsd3 commented 3 years ago

Good to know. I put Pedro in cc.

Hi Pedro, people from Galaxy are considering incorporating your tool to their server.

Em qui., 4 de fev. de 2021 às 07:44, M Bernt notifications@github.com escreveu:

https://github.com/pedronachtigall/MITGARD

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pedronachtigall commented 3 years ago

Hi,

Sorry for the slow response, I had a really busy week.

Thank you @bernt-matthias for considering MITGARD to be integrated into the Galaxy platform. Thank you @dougsd3 for cc me about this issue.

What should we need to make it happen?

Best, Pedro

bernt-matthias commented 3 years ago

Hi @pedronachtigall

What should we need to make it happen?

pedronachtigall commented 3 years ago

Hi @bernt-matthias

MITGARD needs to be added to bioconda.

A quick look on your github page showed me that you use the ete3 module to download taxonomy. If I remember correctly this is then stored in the home directory. This won't work, i.e. for Galaxy this would need to be configurable. We have a data manager that downloads the taxdump from the NCBI ftp. Could MITGARD be congigured to work on such a taxdump?

Are there any other databases involved?

bgruening commented 3 years ago

@pedronachtigall for Bioconda we have here some documentation: https://bioconda.github.io/contributor/index.html let me know if you need help.

bernt-matthias commented 3 years ago

I can implement MITGARD with an option to turn on/off the MitoZ software and make it off by default. Then, Galaxy may not allow the user to set this option on. What do you think?

Yep, this is possible (you do not need to disable MitoZ by default .. but this is up to you).

But it seems possible to add MitoZ to bioconda as well (someone already tried https://github.com/bioconda/bioconda-recipes/pull/22334). They have (kind of) releases: https://github.com/linzhi2013/MitoZ/blob/master/version_2.3/release_MitoZ_v2.3.tar.bz2 which could be used. Lets see if we can reactivate this. Which version of MitoZ would you need?

But we can go without MitoZ it the first place and readd it later...

bernt-matthias commented 3 years ago
bgruening commented 3 years ago

We are currently working on mitohifi which is using mitofinder. Mitofinder has a few problems to deploy it in conda, so we have a Docker image for it, which we also use for mitohifi.

dougsd3 commented 3 years ago

Great news

Thanks !!!

Em qui, 27 de mai de 2021 06:17, Björn Grüning @.***> escreveu:

We are currently working on mitohifi which is using mitofinder. Mitofinder has a few problems to deploy it in conda, so we have a Docker image for it, which we also use for mitohifi.

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pedronachtigall commented 3 years ago

Hi @bernt-matthias and @bgruening ,

After a long time, I had a chance to work to get MITGARD as a docker repository and modify MITGARD to have MitoZ as an option. Now MITGARD can be used through docker docker pull pedronachtigall/mitgard:latest. The Dockerfile can be also found in MITGARD repository. Is it enough to implement MITGARD into Galaxy? If we still need to make it available through conda, I already have a meta.yaml with all dependencies (except for MitoZ, which is optional now.

Can you help me to design a build.sh file to have it installed through conda? https://github.com/pedronachtigall/MITGARD

I will appreciate your help.

Best regards, Pedro

bernt-matthias commented 3 years ago

Wonderful @pedronachtigall . conda would be super convenient for Galaxy. Seems that the build file only needs to copy the python scripts to ${PREFIX}/bin. Also you will need a release on your github project.

You may just open a PR (make it a draft) on bioconda recipes and ping me.

Btw, at the training week of the Galaxy community conference (end of June) there is a tutorial explaining how to get a running Galaxy tool starting with conda, over tool building and testing ...

pedronachtigall commented 3 years ago

Hi @bernt-matthias , I already release the first version of MITGARD and upload build.sh and meta.yaml files into recipes of bioconda repository. I pig you into the PR. Hope it works fine.

FYI, I also take the opportunity to add a PR for another tool named CodAn (https://github.com/pedronachtigall/CodAn), which I also want to have it easily installed through conda.

Let me know if everything is fine, or if I need to change something in the files.

pedronachtigall commented 3 years ago

Hi, MITGARD is ready to go through Conda installation: https://anaconda.org/bioconda/mitgard Just let me know if you need anything else to have it integrated into the Galaxy.

pedronachtigall commented 3 years ago

Hi, do you have any news about adding MITGARD into Galaxy? Is the tutorial available (the tutorial mentioned in the "training week of the Galaxy community")?

o-william-white commented 3 years ago

@bernt-matthias I have seen that GetOrganelle has been requested for galaxy and some work has already been done https://github.com/Kinggerm/GetOrganelle/issues/64

Just wondering it is going to be added to Galalxy toolshed? Apologies if I have missed it

bernt-matthias commented 3 years ago

Hi @o-william-white unfortulately I have not found time to work on this. But I'm happy to help if someone wants to jump in and submit a tool wrapper.

o-william-white commented 3 years ago

Hi @bernt-matthias, thank you for letting me know, I've been having a look at the documentation about how to set up a tool wrapper. If I make any progress I will let you know.

o-william-white commented 2 years ago

Hi @bernt-matthias, just wanted to let you know that I have started working on a wrapper for get organelle. It's been a bit of a learning curve but I have a wrapper which works with the most basic parameters in get organelle. It have uploaded it here https://github.com/o-william-white/galaxy_wrappers/blob/main/get_organelle_from_reads/get_organelle_from_reads.xml

My plan is to continue to develop this to include more advanced parameters for fine tuning analyses.

It would be great if this could eventually be included in the IUC tools, I expect with some edits from people more experienced in writing wrappers for galaxy. Do you think this would be possible? I haven't contributed code before so if you have any reccomendations or suggestions on how best to do this please do let me know.

Best wishes Ollie

bernt-matthias commented 2 years ago

Hi @o-william-white wonderful. Maye just open a PR to the IUC with the current state. Then we can give some suggestions.

o-william-white commented 2 years ago

Hi @bernt-matthias thanks for the reply. I just wanted to check a few things to make sure I understand as I havent done this before. A PR is a pull resquest? To do this, I create a fork of the tools-iuc repository, add my xml wrapper to the tools folder and then create a pull request. Presumably this pull request isn't intended to be a finished product, but it will give you the oppertunity to suggest changes? Apologies for checking, just wanted to make sure I didn't do something annoying!

bernt-matthias commented 2 years ago

@o-william-white exactly. Don't forget the .shed.yaml file, otherwise tests won't run.

o-william-white commented 2 years ago

@bernt-matthias awesome, thank you. I will use a .shed.yaml file from another tool as a template and hopefully that works

o-william-white commented 2 years ago

@bernt-matthias I have added the PR https://github.com/galaxyproject/tools-iuc/pull/4455 hopefully this is all ok! Thanks for the advice