# HG changeset patch
# User peterjc
# Date 1496853219 14400
# Node ID 0785a6537f3e66f7d8086a6b2ed7875336b55c0a
# Parent  1291ed21789fc0d1ee2176f31983a51cd4cd121f
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 6405ba93fcec7ea93452bf54d559c7507ee7a57c

diff -r 1291ed21789f -r 0785a6537f3e tools/mira4_0/mira4.py
--- a/tools/mira4_0/mira4.py	Fri Jun 02 11:22:01 2017 -0400
+++ b/tools/mira4_0/mira4.py	Wed Jun 07 12:33:39 2017 -0400
@@ -25,7 +25,7 @@
     # however there is some pipe error when doing that here.
     cmd = [mira_binary, "-v"]
     try:
-        child = subprocess.Popen(cmd,
+        child = subprocess.Popen(cmd, universal_newlines=True,
                                  stdout=subprocess.PIPE,
                                  stderr=subprocess.STDOUT)
     except Exception as err:
diff -r 1291ed21789f -r 0785a6537f3e tools/mira4_0/mira4_bait.py
--- a/tools/mira4_0/mira4_bait.py	Fri Jun 02 11:22:01 2017 -0400
+++ b/tools/mira4_0/mira4_bait.py	Wed Jun 07 12:33:39 2017 -0400
@@ -19,7 +19,7 @@
     # however there is some pipe error when doing that here.
     cmd = [mira_binary, "-v"]
     try:
-        child = subprocess.Popen(cmd,
+        child = subprocess.Popen(cmd, universal_newlines=True,
                                  stdout=subprocess.PIPE,
                                  stderr=subprocess.STDOUT)
     except Exception as err:
@@ -88,7 +88,7 @@
 start_time = time.time()
 try:
     # Run MIRA
-    child = subprocess.Popen(cmd_list,
+    child = subprocess.Popen(cmd_list, universal_newlines=True,
                              stdout=subprocess.PIPE,
                              stderr=subprocess.STDOUT)
 except Exception as err:
diff -r 1291ed21789f -r 0785a6537f3e tools/mira4_0/mira4_convert.py
--- a/tools/mira4_0/mira4_convert.py	Fri Jun 02 11:22:01 2017 -0400
+++ b/tools/mira4_0/mira4_convert.py	Wed Jun 07 12:33:39 2017 -0400
@@ -29,7 +29,8 @@
     # Avoid using shell=True when we call subprocess to ensure if the Python
     # script is killed, so too is the child process.
     try:
-        child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        child = subprocess.Popen(cmd, universal_newlines=True,
+                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     except Exception as err:
         sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
     # Use .communicate as can get deadlocks with .wait(),
diff -r 1291ed21789f -r 0785a6537f3e tools/mira4_0/mira4_make_bam.py
--- a/tools/mira4_0/mira4_make_bam.py	Fri Jun 02 11:22:01 2017 -0400
+++ b/tools/mira4_0/mira4_make_bam.py	Wed Jun 07 12:33:39 2017 -0400
@@ -12,6 +12,7 @@
 def run(cmd, log_handle):
     try:
         child = subprocess.Popen(cmd, shell=True,
+                                 universal_newlines=True,
                                  stdout=subprocess.PIPE,
                                  stderr=subprocess.STDOUT)
     except Exception as err:
diff -r 1291ed21789f -r 0785a6537f3e tools/mira4_0/repository_dependencies.xml
--- a/tools/mira4_0/repository_dependencies.xml	Fri Jun 02 11:22:01 2017 -0400
+++ b/tools/mira4_0/repository_dependencies.xml	Wed Jun 07 12:33:39 2017 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the MIRA datatype definitions (e.g. the MIRA Assembly Format).">
-    <repository changeset_revision="080d217544b0" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="3fc6ff47a3b1" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>