Differences

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--- structure-software [2017/02/21 08:28] – joguya
+++ structure-software [2017/05/04 06:40] – aorth
@@ Line 7: / Line 7: @@
   * Latest version: 2.3.4
   * Added: June, 2014
-  * Link: http://pritchardlab.stanford.edu/structure.html
+  * Link: https://web.stanford.edu/group/pritchardlab/structure.html
 ===== Usage =====
@@ Line 70: / Line 70: @@
     readonly EXTRAPARAMS=$3
     readonly INFILE=$4
-    readonly CWD=$PWD
 fi
+readonly CWD=$PWD
 for rep in $(seq 1 $REPS)
@@ Line 78: / Line 79: @@
         do
 	echo "REP: $rep POP: $pop"
+    outfile="$SCRATCH_DIR/$(basename $INFILE)_K${pop}-rep${rep}"
                 sbatch <<BATCH_SCRIPT
 #!/bin/env bash
@@ Line 83: / Line 85: @@
 #SBATCH -J structure
 #SBATCH -p batch
-#SBATCH -w taurus
+#SBATCH -w mammoth
 module load structure/2.3.4
@@ Line 94: / Line 96: @@
 # run structure with a different random seed for each run
-outfile="$SCRATCH_DIR/$(basename $INFILE)_K${pop}-rep${rep}"
 structure-gcc492 -m $MAINPARAMS -e $EXTRAPARAMS -K $POPULATION  -D $RANDOM -i $INFILE -o $outfile
 # copy back results to data dir.
-mv -v ${outfile} $CWD/
+mv -v ${SCRATCH_DIR} $CWD
-echo "Your results are in: $CWD directory
+echo "Your results are in: $CWD directory"
 BATCH_SCRIPT