Common: Use temporary directory when invoking circos

hmf-common/pom.xml

@@ -62,6 +62,18 @@
             <artifactId>junit</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.16.1</version>
+            <scope>compile</scope>
+        </dependency>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.16.1</version>
+            <scope>compile</scope>
+        </dependency>
     </dependencies>
 
     <build>

hmf-common/src/main/java/com/hartwig/hmftools/common/circos/CircosExecution.java

@@ -2,8 +2,12 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.List;
+import java.util.Map;
 
+import org.apache.commons.io.FileUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
@@ -44,10 +48,22 @@ public Integer generateCircos(
 
         LOGGER.info(String.format("generating " + outputFile + " via command: %s", String.join(" ", command)));
 
+        ProcessBuilder processBuilder = new ProcessBuilder(command);
+        Map<String, String> environment = processBuilder.environment();
+
+        // Circos writes the temporary file circos.colorlist. However, this file would be overwritten multiple times when invoking circos
+        // from multiple threads which results in a race condition. We make sure that circos writes to different temporary directories to
+        // avoid this race condition
+        Path tempDir = Files.createTempDirectory("circos");
+        environment.put("TMPDIR", tempDir.toString());
+
         // must redirect error stream to stdout, as circos print some errors to stdout
-        Process process = new ProcessBuilder(command).redirectErrorStream(true).start();
+        Process process = processBuilder.redirectErrorStream(true).start();
+
         int result = process.waitFor();
 
+        FileUtils.deleteDirectory(tempDir.toFile());
+
         if(result != 0)
         {
             System.err.print(new String(process.getInputStream().readAllBytes()));