Aligned cli and submit

cli_01b.r

@@ -55,6 +55,14 @@ options <- list (
     default = default.nperm,
     help    = "How many permutations?",
     metavar = "4"
+  ), 
+  make_option(
+    opt_str = c("-s", "--start.round"),
+    dest    = "start.round",
+    type    = "integer",
+    default = NA,
+    help    = "Which start round?",
+    metavar = "4"
   )
 )
 
@@ -65,7 +73,7 @@ parser <- OptionParser(
        epilogue    = "use with caution, the awesomeness might slap you in the face!"
 )
 
-cli <- parse_args(parser, positional_arguments = 6)
+cli <- parse_args(parser, positional_arguments = 5)
 
 # ------------------------------------------------------------------------------
 # assign a few shortcuts
@@ -76,7 +84,7 @@ traits.path  	 <- cli$args[2]
 output  	     <- cli$args[3]
 myfunction   	 <- cli$args[4]
 combinations   <- cli$args[5]
-start.round    <- cli$args[6]
+start.round    <- cli$options$start.round
 max.inter.t    <- cli$options$max.inter.t
 chunkn         <- cli$options$chunkn
 chunk.i        <- cli$options$chunk.i
@@ -89,5 +97,5 @@ ncores         <- cli$options$ncores
 
 source("01b_MesobromionCluster.R")
 
-Mesobromion(species.path, traits.path, output, myfunction, combinations, max.inter.t, 
-            chunkn, chunk.i, nperm, ncores)
+Mesobromion(species.path, traits.path, output, myfunction, combinations, start.round
+            max.inter.t, chunkn, chunk.i, nperm, ncores)

submit_01b.sh

@@ -6,8 +6,8 @@
 #$ -o /work/$USER/$JOB_NAME-$JOB_ID.log
 #$ -j y
 
-#$ -l h_rt=00:45:00:00
-#$ -l h_vmem=1G
+#$ -l h_rt=00:50:00:00
+#$ -l h_vmem=2G
 
 #$ -pe smp 24-32
 
@@ -25,9 +25,10 @@ Rscript \
     --chunkn 32 \
     --nperm 999 \
     --ncores ${NSLOTS:-1} \
+    --start.round 4 \
     /data/splot/HIDDEN/species.out.10perc.txt \
     /data/splot/HIDDEN/traits.out.10perc.txt \
     "$output" \
     "get.corXY.bootstrap" \
     "sequential" \
-    4
+