Merge pull request #226 from SysBioChalmers/feat/runDLKcatFromDocker

feat: run DLKcat from a Docker image

src/geckomat/gather_kcats/runDLKcat.m

@@ -57,7 +57,7 @@ function runDLKcat(DLKcatFile, modelAdapter, DLKcatPath, pythonPath, pipPath)
     packageURL = 'https://github.com/SysBioChalmers/GECKO/raw/dlkcatPackage/dlkcat.zip';
     %packageURL = 'https://github.com/SysBioChalmers/GECKO/releases/download/v3.0.0/dlkcat_package.zip';
     websave(fullfile(DLKcatPath,'dlkcat_package.zip'),packageURL);
-    unzip(fullfile(DLKcatPath,'dlkcat_package.zip'),DLKcatPath);
+    unzip(fullfile(DLKcatPath,'dlkcat_package.zip'),geckoPath);
     delete(fullfile(DLKcatPath,'dlkcat_package.zip'));
 end
 
@@ -76,6 +76,7 @@ function runDLKcat(DLKcatFile, modelAdapter, DLKcatPath, pythonPath, pipPath)
             MACZPROFILEPATH = 'set';
         catch
         end
+        setenv('PATH', strcat('/usr/local/bin', ':', getenv("PATH")));
     end
 end
 

src/geckomat/gather_kcats/runDLKcatFromDocker.m

@@ -0,0 +1,111 @@
+function runDLKcatFromDocker(deleteImage, DLKcatFile, modelAdapter, DLKcatPath)
+% runDLKcatFromDocker
+%   Runs DLKcat to predict kcat values from a Docker image
+%
+% Input
+%   deleteImage      true or false if delete the docker image tar.gz file.
+%                   (Optional, default = false)
+%   DLKcatFile      path to the DLKcat.tsv file (including file name), as
+%                   written by writeDLKcatFile. Once DLKcat is succesfully
+%                   run, the DLKcatFile will be overwritten with the DLKcat
+%                   output. Optional, otherwise the file location will be
+%                   assumed to be in the model-specific 'data' sub-folder
+%                   taken from modelAdapter (e.g.
+%                   GECKO/userData/ecYeastGEM/data/DLKcat.tsv)
+%   modelAdapter    a loaded model adapter. (Optional, will otherwise use
+%                   the default model adapter)
+%   DLKcatPath      path where DLKcat is/will be installed. (Optional,
+%                   defaults to GECKO/dlkcat)
+%
+%   NOTE: 1. Requires Docker to be installed, and docker desktop running. Visit "https://www.docker.com"
+%         2. Runtime will depend on whether the image is to be downloaded or not.
+
+%Get the GECKO path
+geckoPath = findGECKOroot();
+
+if nargin < 4 || isempty(DLKcatPath)
+    DLKcatPath = fullfile(geckoPath,'dlkcat');
+end
+
+if nargin < 3 || isempty(modelAdapter)
+    modelAdapter = ModelAdapterManager.getDefaultAdapter();
+    if isempty(modelAdapter)
+        error('Either send in a modelAdapter or set the default model adapter in the ModelAdapterManager.')
+    end
+end
+params = modelAdapter.params;
+
+if nargin < 2 || isempty(DLKcatFile)
+    DLKcatFile = fullfile(params.path,'data','DLKcat.tsv');
+end
+
+if nargin < 1 || isempty(DLKcatPath)
+    deleteImage = false;
+end
+
+%% Check and install requirements
+% On Mac, docker might not be properly loaded if MATLAB is started via
+% launcher and not terminal.
+if ismac
+    setenv('PATH', strcat('/usr/local/bin', ':', getenv("PATH")));
+end
+
+% Check if docker is installed
+[checks.docker.status, checks.docker.out] = system('docker --version');
+if checks.docker.status ~= 0
+    error('Cannot find Docker. Make sure it is installed')
+end
+
+% Dowload DLKcat package
+if ~exist(fullfile(DLKcatPath,'DLKcat.py'),'file')
+    if ~exist(fullfile(DLKcatPath),'dir')
+        mkdir(fullfile(DLKcatPath));
+    end
+    disp('=== Downloading DLKcat ...')
+    packageURL = 'https://github.com/SysBioChalmers/GECKO/raw/dlkcatPackage/dlkcat.zip';
+    %packageURL = 'https://github.com/SysBioChalmers/GECKO/releases/download/v3.0.0/dlkcat_package.zip';
+    websave(fullfile(DLKcatPath,'dlkcat_package.zip'),packageURL);
+    unzip(fullfile(DLKcatPath,'dlkcat_package.zip'),geckoPath);
+    delete(fullfile(DLKcatPath,'dlkcat_package.zip'));
+end
+
+currPath = pwd();
+cd(DLKcatPath);
+
+% First check if the Docker image exist
+[checks.image.status, checks.image.out] = system('docker images');
+if checks.image.status == 0 && ~contains(checks.image.out,'dlkcat')
+    % Check if the image file is already dowloaded
+    if ~exist(fullfile(DLKcatPath,'dlkcat_docker.tar.gz'),'file')
+        disp('=== Downloading DLKcat docker image, this may take more than 20 minutes, depending on your internet connection speed...')
+        packageURL = 'https://github.com/SysBioChalmers/GECKO/raw/dlkcatPackage/dlkcat_docker.tar.gz';
+        websave(fullfile(DLKcatPath,'dlkcat_docker.tar.gz'),packageURL);
+    end
+    [checks.dockerload.status, checks.dockerload.out] = system('docker load --input dlkcat_docker.tar.gz');
+    if deleteImage
+        delete(fullfile(DLKcatPath,'dlkcat_docker.tar.gz'));
+    end
+    if checks.dockerload.status ~= 0
+        error('Fail to load the image')
+    end
+elseif checks.image.status ~= 0
+    error('Looks like Docker is installed, but make ensure that the docker desktop app is running.')
+end
+
+% Copy the input file for needed for the docker image to run DLKcat
+copyfile(DLKcatFile,fullfile(DLKcatPath, 'data/DLKcat.tsv'));
+
+disp('=== Running DLKcat prediction, this may take several minutes...')
+% In the next line, pythonPath does not need to be specified, because it is
+% already mentioned when building the virtualenv.
+dlkcat.status = system('docker compose -f docker-compose.yaml up dlkcat-cont', '-echo');
+
+if dlkcat.status == 0
+    movefile('data/DLKcatOutput.tsv',DLKcatFile);
+    cd(currPath);
+else
+    cd(currPath);
+    error('DLKcat encountered an error.')
+end
+
+end