pinellolab / crispr-surf Goto Github PK

Hi Luca,

When trying to run CRISPR-SURF from a local installation, I get the following error message

docker run -v ${PWD}/:/DATA -w /DATA pinellolab/crisprsurf SURF_design

"docker: Error response from daemon: create ${PWD}: "${PWD}" includes invalid characters for a local volume name, only "[a-zA-Z0-9][a-zA-Z0-9_.-]" are allowed. If you intended to pass a host directory, use absolute path."

What is the path for the DATA directory on a local installation, or how can I find it? Sorry I am new to Docker.

Hello
I am using GECKO library and I was wondering how I can get a sgRNA library file for the input.

Does CRISPR-SURP accept paired-end FASTQ? If yes, what's the correct SURF_count command?

Any possibility of some documentation for installing the command line version outside of docker?

Hello,

I am trying to analyze a data set with 6 replicates but for some reason the program seems to stall after 4 hours during the 1000 simulations step. The cpu usage according to docker suddenly drops from 400% to 0.1% and the memory usage drastically drops as well. It has been stuck like this for over 12 hours. Is there a way to work around this? It works fine with 3 replicates but I would like to do all 6 if possible.