TASK-5513 Fix the Docker image configuration for OpenCGA analysis #2389
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…onfiguration file, #TASK-5513
jtarraga
changed the title
j-coll
previously approved these changes
Feb 7, 2024
| @@ -140,7 +141,16 @@ protected void run() throws Exception { | |||
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| // And finally, link the BW file is necessary | |||
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Instead of manually "moving and linking" the file, there is a method OpenCgaTool#moveFile that you could use, which moves, links and associates the file with the job
| // Execute R script in docker | ||
| AbstractMap.SimpleEntry<String, String> outputBinding = new AbstractMap.SimpleEntry<>(outDir.toAbsolutePath().toString(), | ||
| "/data/output"); | ||
| String rParams = "R CMD Rscript --vanilla /data/input/" + inputFile.getName(); | ||
| try { | ||
| String cmdline = DockerUtils.run(MutationalSignatureLocalAnalysisExecutor.R_DOCKER_IMAGE, null, outputBinding, rParams, null); | ||
| System.out.println("Docker command line: " + cmdline); |
| @@ -21,6 +21,9 @@ | |||
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| public abstract class PedigreeGraphAnalysisExecutor extends OpenCgaToolExecutor { | |||
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| public static final String ID = "pedigree-graph"; | |||
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I think that usually ID+Description constants are in the main analysis, rather than in the executor
| /** | ||
| * Created by jtarraga on 24/01/24. | ||
| */ | ||
| public class Docker { |
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I'd have called this "DockerConfig" or something different, as "Docker" alone might be confusing
Resolve conflicts: opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentCoverageAnalysis.java opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/IBDComputation.java opencga-analysis/src/main/java/org/opencb/opencga/analysis/individual/qc/IndividualQcUtils.java opencga-analysis/src/main/java/org/opencb/opencga/analysis/individual/qc/InferredSexComputation.java opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java opencga-analysis/src/test/java/org/opencb/opencga/analysis/alignment/AlignmentAnalysisTest.java opencga-core/src/main/java/org/opencb/opencga/core/config/Analysis.java
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Add Docker images into the configuration file