analysis: update to changes, #TASK-7619, #TASK-7037

Author: jtarraga

opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/regenie/RegenieStep1WrapperAnalysis.java

@@ -194,13 +194,11 @@ private void prepareWalkerDocker() throws ToolException {
             FileUtils.copyFile(phenoFile.toFile(), dataDir.resolve(PHENO_FILENAME).toFile());
             // Copy Python scripts and files
             Path pythonDir = dataDir.resolve("python");
-            List<String> filenames = Arrays.asList("requirements.txt", "variant_walker.py");
+            List<String> filenames = Arrays.asList("requirements.txt", "variant_walker.py", "regenie_walker.py");
             for (String filename : filenames) {
                 FileUtils.copyFile(getOpencgaHome().resolve("analysis/regenie/" + filename).toAbsolutePath(),
                         pythonDir.resolve(filename));
             }
-            FileUtils.copyFile(getOpencgaHome().resolve("analysis/regenie/regenie_walker.py"),
-                    pythonDir.resolve("regenie_walker.py"));
             // Copy step1 results (i.e., prediction files) and update the paths within the file step1_pred.list
             Path predDir = dataDir.resolve("pred");
             if (!Files.exists(Files.createDirectories(predDir))) {

opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/regenie/RegenieStep1WrapperAnalysisExecutor.java

@@ -85,7 +85,7 @@ public String getDockerImageName() throws ToolException {
 
     @Override
     public String getDockerImageVersion() {
-        return GitRepositoryState.getInstance().getBuildVersion();
+        return "4.0.0-SNAPSHOT"; //GitRepositoryState.getInstance().getBuildVersion();
     }
 
     public String getStudy() {

opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/regenie/RegenieUtils.java

@@ -119,7 +119,7 @@ public static String buildAndPushDocker(Path dataDir, String dockerName, String
             dockerRepoVersion = Instant.now().getEpochSecond() + "-" + (random.nextInt(9000) + 1000);
         }
 
-        Path dockerBuildScript = opencgaHome.resolve("analysis/resources/walker/custom-tool-docker-build.py");
+        Path dockerBuildScript = opencgaHome.resolve("analysis/resources/common/tool-docker-builder.py");
         Command dockerBuild = new Command(new String[]{"python3", dockerBuildScript.toAbsolutePath().toString(),
                 "--custom-tool-dir", dataDir.toAbsolutePath().toString(),
                 "--base-image", "joaquintarraga/opencga-regenie:" + GitRepositoryState.getInstance().getBuildVersion(),

opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/OpenCGATestExternalResource.java

@@ -304,20 +304,20 @@ public Path isolateOpenCGA() throws IOException {
             }
         }
 
-        // regenie
+        // Regenie analysis
         Path dockerPath = Files.createDirectories(opencgaHome.resolve("analysis/regenie")).toAbsolutePath();
-        filenames = Arrays.asList("regenie_walker.py", "regenie_step1.sh");
+        filenames = Arrays.asList("regenie_walker.py", "regenie_step1.sh", "requirements.txt", "variant_walker.py");
         for (String filename : filenames) {
             try (FileInputStream inputStream = new FileInputStream("../opencga-app/app/analysis/regenie/" + filename)) {
                 Files.copy(inputStream, dockerPath.resolve(filename), StandardCopyOption.REPLACE_EXISTING);
             }
         }
 
-        // walker
-        dockerPath = Files.createDirectories(opencgaHome.resolve("analysis/resources/walker")).toAbsolutePath();
-        filenames = Arrays.asList("custom-tool-docker-build.py", "requirements.txt", "variant_walker.py");
+        // common
+        dockerPath = Files.createDirectories(opencgaHome.resolve("analysis/resources/common")).toAbsolutePath();
+        filenames = Arrays.asList("tool-docker-builder.py");
         for (String filename : filenames) {
-            try (FileInputStream inputStream = new FileInputStream("../opencga-app/app/analysis/resources/walker/" + filename)) {
+            try (FileInputStream inputStream = new FileInputStream("../opencga-app/app/analysis/resources/common/" + filename)) {
                 Files.copy(inputStream, dockerPath.resolve(filename), StandardCopyOption.REPLACE_EXISTING);
             }
         }