remove pre command as the purpose was to load environment modules, but they...

remove pre command as the purpose was to load environment modules, but they are loaded in a subshell

Snakefile

@@ -76,8 +76,6 @@ def prepare_environment(stepname):
     if not os.path.exists(bench):
         os.makedirs(bench)
 
-    if stepname in config and 'pre' in config[stepname]:
-        shell(config[stepname]['pre'])
     return out, os.path.join(out, '%s.log' % stepname)
 
 

src/config.imp.json

@@ -15,7 +15,6 @@
       "db_path": "db"
     },
     "Preprocessing": {
-      "pre": "echo '//LOADING PREPROCESSING MODULE'",
       "filtering": true,
       "trimmomatic": {
           "adapter": "TruSeq3",
@@ -33,7 +32,6 @@
       }
     },
     "Assembly": {
-      "pre": "echo '//LOADING ASSEMBLY MODULE'",
       "idba_ud": {
           "mink": 25,
           "maxk": 95,
@@ -42,7 +40,6 @@
       }
     },
     "Analysis": {
-      "pre": "echo '//LOADING ANALYSIS MODULE'",
       "vizbin": {
           "dimension": 50,
           "length": 5,
@@ -53,7 +50,6 @@
       }
     },
     "Util": {
-      "pre": "echo '//LOADING UTIL MODULE'"
     },
     "human_filtering": {
         "filter": "chr21",