AlphaFold
1. INCD Local Installation
The INCD team prepare a local installation of AlphaPhold using a container based on UDOCKER (instead of DOCKER) and includes the Genetic Database.
The local installation provide the AlphaFold version 2.1.1 over a container based on Ubuntu 18.04 distribution with cuda-11.0 and cudnn-8.
The main resource target of AlphaFold is the GPU but the application also execute only on the CPU although the performance is substantially worst, see the Run Exemples section bellow.
1.1 Environment
The environment is activate with command
$ module load udocker/alphaphold/2.1.1
this will activate automatically a virtual environment ready to start the AlphaFold container throught the python script run_udocker.py.
1.2 Data Base Location
The Genetic Database is installed bellow the filesystem directory
/users3/data/alphafold
on read-only mode, upgrades may be requested using the helpdesk@incd.pt address.
1.3 run_udocker.py Script
The run_udocker.py script was adapted from the run_docker.py script normally used by AlphaFold with the docker container technology.
The run_udocker.py accept the same options as the run_docker.py script with a few minor changes that we hope it will facilitate user interaction:
- environment variable DOWNLOAD_DIR points to the default local genetic database, the user may change the content, the option --data_dir takes precedence over this environment variable;
- option --data_dir: is optional and points to the local genetic database by default, takes prececence over the environment variabal DOWNLOAD_DIR;
- the output dir points to a subdirectory output on the working directory by default instead of /tmp/alphafold/output;
- environment variable OUTPUT_DIR may be used to overwirte the default output directory;
- option --output_dir may be used to select a different output directory and takes precedence over the environment variable OUTPUT_DIR and the default output location.