More Config and init cleanup

scripts/common.conf

@@ -7,6 +7,13 @@ PROJECT_DIR=${HOME}/angsd-wrapper
 ANGSD_DIR=${PROJECT_DIR}/angsd
 #   Where the scripts are stored
 SCRIPTS_DIR=${PROJECT_DIR}/scripts
+#   Where we will store results
+RESULTS_DIR=${SCRIPTS_DIR}/results
+#   A temporary directory
+TEMP_DIR=${SCRIPTS_DIR}/temp
+#   Where we will store data
+#       How is this different from data/ in the main directory??
+DATA_DIR=${SCRIPTS_DIR}/data
 #   Where ngsPopGen is stored
 NGS_POPGEN_DIR=${PROJECT_DIR}/ngsPopGen
 

scripts/init.sh

@@ -1,2 +1,8 @@
 #!/bin/sh
-mkdir ./results/ ./temp/ ./data/
+#   Script to create the directory structure for angsd-wrapper
+source common.conf
+#   test if our directory is writable (it should be!)
+if [ -w `dirname ${PROJECT_DIR}` ]
+    then mkdir -p ${RESULTS_DIR} ${TEMP_DIR} ${DATA_DIR}
+    else echo "Directory is not writable!"; exit 1
+fi