Run From Anywhere

[BrandonFrenz]

This PR updates all the relevant code so that jobs can be launched from any directory as long as the proper environment variables are set. It is intended to be fully backward compatible with the existing method of running from the main directory.

This PR also includes a docker file capable of building a container that can run RoseTTAFoldAllAtom, as well as an update to the READ.ME which describes how to use it and a new directory with an example for how to run a job inside the docker container.

[wehs7661]

Hi @BrandonFrenz ! This looks very useful! Has it been made possible to run RFAA from anywhere or in a docker container on your branch? Thanks a lot!

[BrandonFrenz]

Hey @wehs7661. I'm not sure if you're asking whether it's possible to use this code without using a docker container or whether a docker container exists in this branch that will work. The answer is yes to both. There is a docker file that builds the image you will need included in this branch, you can see an example of how to run it in the examples directory of this branch.

If you want to run it without a docker container but get rid of the requirement to run from the main repository you need to set the following 3 environment variables to the proper database paths. export DB_UR30=$db_path/UniRef30_2020_06 export DB_BFD=$db_path/bfd/ export BLASTMAT=$db_path/blast-2.2.26/data/

[wehs7661]

Hi @BrandonFrenz , thanks for the prompt reply!

I'm not sure if you're asking whether it's possible to use this code without using a docker container or whether a docker container exists in this branch that will work.

I was actually asking about both. Sorry for not being clear! Good to know that both are working!

you need to set the following 3 environment variables to the proper database paths.

This works perfectly for me. Thanks so much!

[BrandonFrenz]

Glad to hear it!