AutoGrow4 is an open-source program for semi-automated computer-aided drug discovery. It uses a genetic algorithm to evolve predicted ligands on demand and so is not limited to a virtual library of pre-enumerated compounds. AutoGrow4 is a useful tool for generating entirely novel drug-like molecules and for optimizing preexisting ligands.
I am writing to seek assistance with an issue I am encountering while testing Autogrow4 on a sample data with Docker. When I execute the command "sudo python3 autogrow_in_docker.py -j ./examples/sample_autogrow_docker_json.json" I obtain the following:
This script builds a docker for AutoGrow4 and runs AutoGrow4 within the docker. The setup may take a few minutes the first time being run and AutoGrow may take a long time depending on the settings.
Handling files
copying files into temp directory: temp_userfiles
/Users/eliechemouni/Desktop/Columbia/Capstone/autogrow4/docker/Outputfolder/Run
There are no previous runs in this directory.
Starting a new run named Run_0.
The Run number is: 0
The Run folder path is: /Users/eliechemouni/Desktop/Columbia/Capstone/autogrow4/docker/Outputfolder/Run_0/
Creating new docker image for AutoGrow4
Attempting to create the docker container. If 1st time running this script it may take a few minutes. Output details are piped to: /Users/eliechemouni/Desktop/Columbia/Capstone/autogrow4/docker/output_and_log_dir/log.txt
[+] Building 0.6s (1/2) docker:desktop-linux
[+] Building 0.7s (2/2) FINISHED docker:desktop-linux
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 2.34kB 0.0s
=> ERROR [internal] load metadata for docker.io/library/ubuntu:18.04 0.6s
[internal] load metadata for docker.io/library/ubuntu:18.04:
Dockerfile:2
1 | # Get the base image from ubuntu
2 | >>> FROM ubuntu:18.04
3 | RUN rm ~/.docker/config.json
4 | RUN docker login
ERROR: failed to solve: ubuntu:18.04: error getting credentials - err: exit status 1, out: ``
Running AutoGrow4 in Docker
docker run --rm -it -v /Users/eliechemouni/Desktop/Columbia/Capstone/autogrow4/docker/Outputfolder/:/Outputfolder/ autogrow4 --name autogrow4 --Run_0
Unable to find image 'autogrow4:latest' locally
2024/03/17 20:05:38 must use ASL logging (which requires CGO) if running as root
docker: Error response from daemon: pull access denied for autogrow4, repository does not exist or may require 'docker login': denied: requested access to the resource is denied.
I am writing to seek assistance with an issue I am encountering while testing Autogrow4 on a sample data with Docker. When I execute the command "sudo python3 autogrow_in_docker.py -j ./examples/sample_autogrow_docker_json.json" I obtain the following:
This script builds a docker for AutoGrow4 and runs AutoGrow4 within the docker. The setup may take a few minutes the first time being run and AutoGrow may take a long time depending on the settings.
Handling files copying files into temp directory: temp_userfiles /Users/eliechemouni/Desktop/Columbia/Capstone/autogrow4/docker/Outputfolder/Run There are no previous runs in this directory. Starting a new run named Run_0. The Run number is: 0 The Run folder path is: /Users/eliechemouni/Desktop/Columbia/Capstone/autogrow4/docker/Outputfolder/Run_0/
Creating new docker image for AutoGrow4
Attempting to create the docker container. If 1st time running this script it may take a few minutes. Output details are piped to: /Users/eliechemouni/Desktop/Columbia/Capstone/autogrow4/docker/output_and_log_dir/log.txt
[+] Building 0.6s (1/2) docker:desktop-linux [+] Building 0.7s (2/2) FINISHED docker:desktop-linux => [internal] load build definition from Dockerfile 0.0s => => transferring dockerfile: 2.34kB 0.0s => ERROR [internal] load metadata for docker.io/library/ubuntu:18.04 0.6s
[internal] load metadata for docker.io/library/ubuntu:18.04: Dockerfile:2
1 | # Get the base image from ubuntu 2 | >>> FROM ubuntu:18.04 3 | RUN rm ~/.docker/config.json 4 | RUN docker login
ERROR: failed to solve: ubuntu:18.04: error getting credentials - err: exit status 1, out: ``
View build details: docker-desktop://dashboard/build/desktop-linux/desktop-linux/64etxeryjvfovizz1lb1963ly
Running AutoGrow4 in Docker docker run --rm -it -v /Users/eliechemouni/Desktop/Columbia/Capstone/autogrow4/docker/Outputfolder/:/Outputfolder/ autogrow4 --name autogrow4 --Run_0 Unable to find image 'autogrow4:latest' locally 2024/03/17 20:05:38 must use ASL logging (which requires CGO) if running as root docker: Error response from daemon: pull access denied for autogrow4, repository does not exist or may require 'docker login': denied: requested access to the resource is denied.