Final modifications for SGE cluster - thanks to Nicolas Rodriguez!

README.md

@@ -1,3 +1,7 @@
+## Summary
+
+This script is dedicated to allow one to quickly and efficiently run a Copasi parameter estimation task on a computing cluster. Running 1000 parameter estimations in minutes and automatically summarising the results allows you to test a lot of hypothesis in a single day! Please enjoy and fork/pull request if you can see some obvious improvements!
+
 ## Prerequisites
 
 1. [LSF](http://www-03.ibm.com/systems/platformcomputing/products/lsf/) or [SGE](http://www.oracle.com/us/products/tools/oracle-grid-engine-075549.html) cluster
@@ -37,4 +41,4 @@ where **n** is number of parameter estimations and **c** is your cluster queuing
 
 Authors: [Vladimir Kiselev](www.genat.uk), Marija Jankovic
 
-Acknowledgments: Martina Fröhlich
+Acknowledgments: Martina Fröhlich, Nicolas Rodriguez

coparaest.sh

@@ -5,9 +5,11 @@ mkdir results out err
 if [ $2 = "lsf" ]; then
    bsub -J "parameter-estimation[1-$1]" -o out/%I -e err/%I sh scripts/parameter-estimation.sh
    bsub -w "ended(parameter-estimation*)" -J "get-obj-values" -o out/get-obj-values -e err/get-obj-values perl scripts/get-obj-values.pl
-   bsub -w "ended(get-obj-values)" -J "analyse-results" -o out/analyse-results -e err/analyse-results /nfs/users/nfs_v/vk6/R-3.2.0/bin/Rscript scripts/analyse-results.R
+   bsub -w "ended(get-obj-values)" -J "analyse-results" -o out/analyse-results -e err/analyse-results Rscript scripts/analyse-results.R
 fi
 
 if [ $2 = "sge" ]; then
- 		echo "sh scripts/job.sh" | qsub -t 1-$1 -cwd -V -o out/%I -e err/%I
+    echo "sh scripts/parameter-estimation.sh" | qsub -t 1-$1 -N "parameter_estimation" -cwd -V -o "out/parameter-estimation-${SGE_TASK_ID}" -e "err/parameter-estimation-${SGE_TASK_ID}"
+    echo "perl scripts/get-obj-values.pl" | qsub -hold_jid "parameter_estimation"  -N "get_obj_values" -cwd -V -o out/get-obj-values -e err/get-obj-values
+    echo "Rscript scripts/analyse-results.R" | qsub -hold_jid "get_obj_values"  -N "analyse_results" -cwd -V  -o out/analyse-results -e err/analyse-results
 fi

scripts/parameter-estimation.sh

@@ -1,5 +1,11 @@
-mkdir results/$LSB_JOBINDEX
-cp model/* results/$LSB_JOBINDEX
-cd results/$LSB_JOBINDEX
+JOB_INDEX=${LSB_JOBINDEX}
+
+if [ "x${LSB_JOBINDEX}" == "x" ]; then
+    JOB_INDEX=${SGE_TASK_ID}
+fi
+
+mkdir results/$JOB_INDEX
+cp model/* results/$JOB_INDEX
+cd results/$JOB_INDEX
 file=`ls *.cps`
-/nfs/users/nfs_v/vk6/COPASI-4.15.95-Linux-64bit/bin/CopasiSE -s $file $file
+CopasiSE -s $file $file