cli and submit

cli_01b.r

+library(optparse)
+
+# ------------------------------------------------------------------------------
+# defaults
+# ------------------------------------------------------------------------------
+
+default.max.inter.t <- 1
+default.nperm <- 99
+# ------------------------------------------------------------------------------
+# parsing arguments
+# ------------------------------------------------------------------------------
+
+options <- list (
+
+  make_option(
+    opt_str = c("-m", "--max.inter.t"),
+    dest    = "max.inter.t",
+    type    = "integer",
+    default = default.max.inter.t,
+    help    = "Max number of interactions for traits",
+    metavar = "4"
+  ),
+  
+  	make_option(
+	  opt_str = c("-n", "--chunkn"),
+	  dest    = "chunkn",
+	  type    = "integer",
+	  default = 1,
+	  help    = "How many chunks?",
+	  metavar = "4"
+	),
+	
+	make_option(
+	  opt_str = c("-i", "--chunk.i"),
+	  dest    = "chunk.i",
+	  type    = "integer",
+	  default = NA,
+	  help    = "Which chunk?",
+	  metavar = "4"
+	), 
+  make_option(
+    opt_str = c("-p", "--nperm"),
+    dest    = "nperm",
+    type    = "integer",
+    default = default.nperm,
+    help    = "How many permutations?",
+    metavar = "4"
+  )
+)
+
+parser <- OptionParser(
+       usage       = "Rscript %prog [options] data dt_beals header output",
+       option_list = options,
+       description = "\nan awesome R script",
+       epilogue    = "use with caution, the awesomeness might slap you in the face!"
+)
+
+cli <- parse_args(parser, positional_arguments = 4)
+
+# ------------------------------------------------------------------------------
+# assign a few shortcuts
+# ------------------------------------------------------------------------------
+
+species.path   <- cli$args[1]
+traits.path  	 <- cli$args[2]
+output  	     <- cli$args[3]
+myfunction   	 <- cli$args[4]
+max.inter.t    <- cli$options$max.inter.t
+chunkn         <- cli$options$chunkn
+chunk.i        <- cli$options$chunk.i
+nperm          <- cli$options$nperm
+
+# ------------------------------------------------------------------------------
+# actual program
+# ------------------------------------------------------------------------------
+
+source("01b_MesobromionCluster.R")
+
+Mesobromion(species.path, traits.path, output, myfunction, max.inter.t, chunkn, chunk.i, nperm)
+
+

submit_01b.sh

+#!/bin/bash
+
+#$ -S /bin/bash
+#$ -N HIDDEN
+
+#$ -o /work/$USER/$JOB_NAME-$JOB_ID-$TASK_ID.log
+#$ -j y
+
+#$ -l h_rt=00:30:00:00
+#$ -l h_vmem=1G
+
+#$ -pe smp 1-1
+
+#$ -cwd
+
+#$ -t 1-1
+
+
+module load R
+
+output=/data/splot/HIDDEN/output/HIDDEN
+
+Rscript \
+    cli_01b.r \
+    --max.inter.t 2 \
+    --chunk.i $SGE_TASK_ID \
+    --chunkn 399 \
+    --nperm 99 \
+    /data/splot/HIDDEN/species.out.10perc.txt \
+    /data/splot/HIDDEN/traits.out.10perc.txt \
+    "$output" \
+    "get.corXY"