analysis: mount fast ephimeral directory, #TASK-6445

Author: pfurio

opencga-analysis/src/main/java/org/opencb/opencga/analysis/tools/OpenCgaDockerToolScopeStudy.java

@@ -12,6 +12,7 @@
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.*;
 import java.util.stream.Stream;
 
@@ -21,6 +22,7 @@ public abstract class OpenCgaDockerToolScopeStudy extends OpenCgaToolScopeStudy
     protected List<AbstractMap.SimpleEntry<String, String>> dockerInputBindings;
     // Directory where temporal input files will be stored
     protected Path temporalInputDir;
+    protected Path ephimeralDir;
 
     protected InputFileUtils inputFileUtils;
 
@@ -30,6 +32,7 @@ protected void check() throws Exception {
         this.dockerInputBindings = new LinkedList<>();
         this.temporalInputDir = Files.createDirectory(getOutDir().resolve(".opencga_input"));
         this.inputFileUtils = new InputFileUtils(catalogManager);
+        this.ephimeralDir = Paths.get("/usr/share/pod");
     }
 
     @Override

opencga-analysis/src/main/java/org/opencb/opencga/analysis/workflow/NextFlowExecutor.java

@@ -191,6 +191,10 @@ protected void run() throws Exception {
             dockerInputBindings.add(new AbstractMap.SimpleEntry<>(path.toString(), path.toString()));
         }
 
+        // Mount ephimeral directory
+        dockerInputBindings.add(new AbstractMap.SimpleEntry<>(ephimeralDir.toAbsolutePath().toString(),
+                ephimeralDir.toAbsolutePath().toString()));
+
         // Write nextflow.config file
         URL nextflowConfig = getClass().getResource("/nextflow.config");
         Path nextflowConfigPath;
@@ -234,7 +238,7 @@ protected void run() throws Exception {
         // Set HOME environment variable to the temporal input directory. This is because nextflow creates a hidden folder there and,
         // when nextflow runs on other dockers, we need to store those files in a path shared between the parent docker and the host
         // TODO: Temporal solution
-        dockerParams.put("-e", "HOME=" + temporalInputDir + " -e OPENCGA_TOKEN=" + getExpiringToken());
+        dockerParams.put("-e", "HOME=" + ephimeralDir + " -e OPENCGA_TOKEN=" + getExpiringToken());
 
 //        dockerParams.put("-e", "HOME=" + temporalInputDir);
 //        dockerParams.put("-e", "OPENCGA_TOKEN=" + getExpiringToken());