scratch scratch scratch (#33)

* helper script to index at start of module3..could be use for all modules

* increment version for cmo_index, etc

* initial commit of cmo_index

* logging

* cmo_split_reads now opens and emits gzips..slow bc native python gzip instead of subprocess zcat

* add logger function

* use bufferereader for speed improvement on gzip

* increment version

* version increment AGAIN

* install cmo_fillout

* longer delay for polling

* speed improvement for split_reads...hopefully...

* increment version for release

* fake gz files for trimgalore

* use args.version

* dumbass tmpdir

* conflicts committed great

* fix tmpdir for diff env, add scratch to mutect

* stupid threads arg

* Update _version.py

Author: lordzappo

bin/cmo_pindel

@@ -40,6 +40,8 @@ def run_pindel(pindel_version, args):
         if value:
             if value == True:
                 command = command + ["--"+argument.replace("_","-")]
+            elif argument=="number_of_threads":
+                command = command + ["--"+argument, value]
             else:
                 command = command + ["--"+argument.replace("_","-"), value]
     print >>sys.stderr, " ".join(command)

cmo/_version.py

@@ -2,5 +2,4 @@
 # This file is originally generated from Git information by running 'setup.py
 # version'. Distribution tarballs contain a pre-generated copy of this file.
 
-__version__ = '1.4.1'
-
+__version__ = '1.4.3'

cmo/gatk.py

@@ -1,29 +1,29 @@
 import os, sys
 from . import util
-
+logger = util.get_logger()
 
 
 
 class Gatk:
-    def __init__(self,version="default", java_version="default", java_args="-Xmx48g -Xms256m -XX:-UseGCOverheadLimit", temp_dir=None, mutect=False):
+    def __init__(self,version="default", java_version="default", java_args="-Xmx48g -Xms256m -XX:-UseGCOverheadLimit -Djava.io.tmpdir=/scratch/", temp_dir="/scratch", mutect=False):
         try:
             if mutect:
                 self.gatk_jar=util.programs["mutect"][version]
             else:
                 self.gatk_jar=util.programs["gatk"][version]
         except KeyError, e:
-            print >>sys.stderr, "Cannot find specified version of gatk in configuration file: %s" % version
+            logger.critical("Cannot find specified version of gatk in configuration file: %s" % version)
             sys.exit(1)
         try: 
             self.java_cmd=util.programs["java"][java_version]
         except KeyError, e:
-            print >>sys.stderr, "Cannot find specified version of java to run gatk with: %s" % java_version
+            logger.critical("Cannot find specified version of java to run gatk with: %s" % java_version)
             sys.exit(1)
         self.temp_dir=None
         if temp_dir:
             self.temp_dir = temp_dir
         self.java_args = java_args 
-        print "selected %s" % self.gatk_jar
+        logger.info("selected %s" % self.gatk_jar)
     def gatk_cmd(self, command, java_args_override=None, command_specific_args={}):
         cmd = [self.java_cmd, self.java_args]
         if(self.temp_dir != None):

test/test_production_commands.py

@@ -28,7 +28,10 @@
 output2 = None
 def setup_module():
     global TEST_TEMP_DIR
-    TEST_TEMP_DIR = tempfile.mkdtemp();
+    if os.path.exists("/scratch"):
+        TEST_TEMP_DIR = tempfile.mkdtemp(dir="/scratch");
+    else:
+        TEST_TEMP_DIR = tempfile.mkdtemp();
     global output
     output= os.path.join(TEST_TEMP_DIR, "output")
     global output2