Attract init

[AnnaKravchenko]

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Checklist

• [ ] Tests added for the new code
• [ ] Documentation added for the code changes
• [x] Does not break licensing
• [ ] Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

Here I have

1. ATTRACT installation guide src/haddock/modules/sampling/attract/install.md
2. A beginning of an [attract], that currently:

• checks ATTRACT installation and env variables
• converts protein and RNA into ATTRACT coarse-grained
• splits RNA into fragments
• prepares folder for the docking
• passes unchanged all-atom protein & RNA to the next module

Related Issue

#1034

Additional Info

On tintin you can use:

export ATTRACTDIR=/trinity/login/arha/tools/attract/bin
export ATTRACTTOOLS=/trinity/login/arha/tools/attract/tools
export LD_LIBRARY_PATH=$ATTRACTDIR:$LD_LIBRARY_PATH
export LIBRARY=/trinity/login/arha/tools/nalib
export RANDSEARCH=/trinity/login/arha/data/ssRNA/randsearch

instead of installing ATTRACT from scratch

[VGPReys]

What about creating a Docker/Singularity container instead with everything inside ? I am thinking here of a solution for the web app.

[rvhonorato]

What about creating a Docker/Singularity container instead with everything inside ? I am thinking here of a solution for the web app.

Not really an option for this case, the third-party software has a hard dependency on py2 while this project is py3. Making a container in which both can co-exist will a bit complex. Makes more sense to containerize the older code and build a wrapper for it.

For attract specifically the maintainer has published an image @ rbps/attract (mobyle2.rpbs.univ-paris-diderot.fr something repository) which can be seamlessly integrated into the web interface as well - it's all the same technology :)

[AnnaKravchenko]

@rvhonorato, can you add here the docker-related script(s) you made, please? And that 1-line call that allows to run /path/attract/tools/reduce.py. Thank you!

[rvhonorato]

un-assigning myself since it seems like this will not go down the containerization route

[AnnaKravchenko]

I would like to continue to work on it, switching from raw ATTRACT code to docker container. Thus let’s keep this branch, even tho it’s pretty old.

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[github-actions[bot]]

This PR was closed because it has been stalled for 5 days with no activity.