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CapraLab / pdbmap

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Inquiry on the Usage #29

Closed JustinaXie closed 3 years ago

JustinaXie commented 3 years ago

Dear Mike and Chris,

Is this pipeline publicly available or just for internal use? Thank you!

Best, Justina

mikesivley commented 3 years ago

Hi Justina, I am no longer involved as a maintainer of the repository so I will defer to Chris.

ChrisMoth commented 3 years ago

Hi Justina,

Sorry for slow reply. I was just in New Haven a few months ago, sorry I did not hear from you earlier :)

The pdbmap library has been a public repository for some time. But, I am aware of no library-only users outside of Vanderbilt.

The psb pipeline repository is accessed by Meilerlab developers at both Vanderbilt Nashville, and U of Leipzig.

An example pipeline output is here:

https://structbio.vanderbilt.edu/~mothcw/2021August05_development/

For production, this is now deployed as a Singularity Container (also Docker is an option). It runs at Washington U. St. Louis (Docker Container on LSF cluster) and has worked at Case Western in Cleveland (Singularity and SLURM cluster), If you might want to run our pipeline at Yale, I'd be delighted to learn a little more about what you are trying to accomplish. "Permission" ultimately comes from Tony Capra and Jens Meiler, my P.I. "bosses".

A little more about me:

http://meilerlab.org/index.php/users/show/u_id/175

Look forward to hearing from you. Direct Email (see link above) usually best for me.

JustinaXie commented 3 years ago

Thank you so much for the information and your kind support! I will reach out through email soon!

Best, Justina