sam_merge: set TMP_DIR and check exit status

tools/samtools/hide_stderr.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+"""A simple script to redirect stderr to stdout when the return code is zero.
+
+See https://bitbucket.org/galaxy/galaxy-central/issue/325/
+
+Currently Galaxy ignores the return code from command line tools (even if it
+is non-zero which by convention indicates an error) and treats any output on
+stderr as an error (even though by convention stderr is used for errors or
+warnings).
+
+This script runs the given command line, capturing all stdout and stderr in
+memory, and gets the return code. For a zero return code, any stderr (which
+should be warnings only) is added to the stdout. That way Galaxy believes
+everything is fine. For a non-zero return code, we output stdout as is, and
+any stderr, plus the return code to ensure there is some output on stderr.
+That way Galaxy treats this as an error.
+
+Once issue 325 is fixed, this script will not be needed.
+"""
+import sys
+import subprocess
+
+#Avoid using shell=True when we call subprocess to ensure if the Python
+#script is killed, so too is the BLAST process.
+try:
+    words = []
+    for w in sys.argv[1:]:
+       if " " in w:
+           words.append('"%s"' % w)
+       else:
+           words.append(w)
+    cmd = " ".join(words)
+    child = subprocess.Popen(sys.argv[1:],
+                             stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+except Exception, err:
+    sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
+    sys.exit(1)
+#Use .communicate as can get deadlocks with .wait(),
+stdout, stderr = child.communicate()
+return_code = child.returncode
+
+if return_code:
+    sys.stdout.write(stdout)
+    # Galaxy seems to hang with large stderr (20000 char fails)
+    max_stderr_len = 15000
+    if len(stderr) > max_stderr_len:
+        stderr_trunc = "%s\n\n... (truncated to reduce size) ...\n\n%s\n" % (stderr[:max_stderr_len/2],
+                                          stderr[-max_stderr_len/2:])
+    else:
+        stderr_trunc = stderr
+    sys.stderr.write(stderr_trunc)
+    sys.stderr.write("Return error code %i from command:\n" % return_code)
+    sys.stderr.write("%s\n" % cmd)
+else:
+    sys.stdout.write(stdout)
+    sys.stdout.write(stderr)

tools/samtools/sam_merge.xml

@@ -3,12 +3,12 @@
   <requirements>
     <requirement type="package">picard</requirement>
   </requirements>
-  <command>
-java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 
+  <command interpreter="python">hide_stderr.py 
+java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 TMP_DIR=$__new_file_path__
       #for $i in $inputs
         I=${i.input}
       #end for 
-    2&gt; $outlog
+      &gt; $outlog
   </command>
   <inputs>
     <param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam"