added dependencies for gaia

conf/gaia_PREPROCESSING_modules.sh

-#!/bin/bash -l
-
-module load BWA 
-module load SAMtools 
-module load BEDTools
-module load OpenBLAS 
-module load Boost/1.53.0-ictce-5.3.0 
-
-module list

conf/userconfig.imp.json

@@ -3,7 +3,7 @@
       "threads": 4
     },
     "Preprocessing": {
-      "pre": "echo '//LOADING PREPROCESSING MODULE: You can write custom shell commands here' && source /home/users/snarayanasamy/repositories/IMP/conf/gaia_PREPROCESSING_modules.sh",
+      "pre": "echo '//LOADING PREPROCESSING MODULE: You can write custom shell commands here' ",
       "filtering": false,
       "trimmomatic": {
       "jarfile": "/mnt/nfs/projects/ecosystem_biology/local_tools/Trimmomatic-0.32/trimmomatic-0.32.jar",
@@ -18,7 +18,7 @@
       }
    },
     "Assembly": {
-      "pre": "echo '//LOADING ASSEMBLY MODULE' && source /home/users/mherold/TOOLS/IMP/conf/gaia_ASSEMBLY_modules.sh"
+      "pre": "echo '//LOADING ASSEMBLY MODULE'"
     },
     "Analysis": {
       "pre": "echo '//LOADING ANALYSIS MODULE'"

modules_to_preload.sh

+#!/bin/bash -l 
+
+
+module load Python
+source env/bin/activate
+
+module load MEGAHIT
+module load BWA 
+module load SAMtools 
+module load BEDTools
+module load OpenBLAS 
+module load Boost/1.53.0-ictce-5.3.0 
+
+export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/idba-1.1.1.icc/bin
+
+module load CAP3
+
+#symbolic links for prokka db 
+module load prokka
+
+export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/tabix-0.2.6
+export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/gkno_launcher/tools/freebayes/bin
+export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/vcftools/bin
+export PERL5LIB=$PERL5LIB:/mnt/nfs/projects/ecosystem_biology/local_tools/vcftools/perl
+export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/Platypus_0.7.9.1
+
+module list