gistfile1.diff

diff --git a/bin/bg7 b/bin/bg7
old mode 100644
new mode 100755
index f5173ba..1b84cab
--- a/bin/bg7
+++ b/bin/bg7
@@ -29,7 +29,8 @@ runs bg7 version 0.9. Params are:
   -G | --genbank_data: xml with extra data for your project needed for .gbk output (things like 
                        locus name, Gen bank division tag, etc). There's a template for this at
                        ${BG7_HOME}/resources/
-                        
+  -t | --threads: how many cores/threads to run the BLAST searches with. Defaults to 1
+
   -h | --help: this message
 
 " >&2
@@ -46,6 +47,7 @@ rnas=""
 genetic_code=""
 output_folder=""
 genbank_data=""
+cores=1
 
 # ## parse input ##
 # Now, we will parse params, override corresponding param var after test, and make some fairly basic sanity checks.
@@ -136,6 +138,13 @@ while [ "$1" != "" ]; do
       fi
       output_folder=$(readlink -f "$1")
     ;;
+    -t | --threads )  shift
+      if [ "$1" = "" ]
+        then
+          echo "Will only use a single core"
+      fi
+      cores="$1"
+    ;;
     -h | --help )           usage
       exit 1
     ;;
@@ -214,9 +223,9 @@ echo "--output_folder ${output_folder}" >> $params_log_file
 # ## BLAST runs ##
 # here we run blast for RNAs and proteins.
 # get number of processors; you need to set this manually for BLAST
-cores=$(grep -c processor /proc/cpuinfo)
-echo "it looks like this machine has ${cores} cores, will use that for blast settings"
-echo "cores used for BLAST: ${cores}" >> $params_log_file
+#cores=$(grep -c processor /proc/cpuinfo)
+#echo "it looks like this machine has ${cores} cores, will use that for blast settings"
+#echo "cores used for BLAST: ${cores}" >> $params_log_file
 # ### RNAs vs contigs run ###
 #
 # first, we run RNAs vs contigs
@@ -394,7 +403,7 @@ EOF
 
 echo "you can take a look at it, if you want: $output_folder/executions.xml"
 # ugly hack, executions.xml should be a param
-cp $BG7_HOME/jar/bg7.jar $output_folder/
+cp $BG7_HOME/jars/BG7.jar $output_folder/bg7.jar
 # run bg7!
 # I will add memory conf through the script later on, no time for this now
 echo "running bg7 now!"