Cleaner method for sbatch to set working dir

Author: bbimber

cluster/src/org/labkey/cluster/pipeline/AbstractClusterExecutionEngine.java

@@ -740,6 +740,11 @@ private ClusterJob getMostRecentClusterSubmission(String jobId, boolean includeI
     }
 
     protected List<String> execute(String command)
+    {
+        return execute(command, null);
+    }
+
+    protected List<String> execute(String command, @Nullable File workDir)
     {
         if (command == null)
         {
@@ -752,7 +757,7 @@ protected List<String> execute(String command)
 
         try
         {
-            Process p = Runtime.getRuntime().exec(command);
+            Process p = Runtime.getRuntime().exec(command, null, workDir);
             try
             {
                 String output = IOUtils.toString(p.getInputStream(), StringUtilsLabKey.DEFAULT_CHARSET);

cluster/src/org/labkey/cluster/pipeline/SlurmExecutionEngine.java

@@ -77,7 +77,7 @@ protected List<String> submitJobToCluster(ClusterJob j, PipelineJob job) throws
         ctx.put("submitScript", getConfig().getClusterPath(submitScript));
         String command = getConfig().getSubmitCommandExpr().eval(ctx);
 
-        List<String> ret = execute(command);
+        List<String> ret = execute(command, submitScript.getParentFile());
         if (ret != null)
         {
             //verify success; create job
@@ -531,7 +531,6 @@ private File createSubmitScript(PipelineJob job) throws PipelineJobException
                     //writer.write("#SBATCH --workdir=\"" + getConfig().getClusterPath(job.getLogFile().getParentFile()) + "\"\n");
 
                     String args = StringUtils.join(getConfig().getJobArgs(outDir, serializedJobFile, job, this), " ");
-                    writer.write("cd " + getConfig().getClusterPath(job.getLogFile().getParentFile()) + "\n");
                     writer.write("srun " + getConfig().getRemoteExecutable() + " " + args);
                 }
             }