Update sandbox for conda and snakemake

sara-nl · Sep 8, 2023 · 0b73100 · 0b73100
1 parent e5ec380
commit 0b73100
Show file tree

Hide file tree

Showing 3 changed files with 24 additions and 8 deletions.
diff --git a/examples/fractals.jdl b/examples/fractals.jdl
@@ -1,7 +1,7 @@
 [
   ParameterStart=0;
   ParameterStep=1;
-  Parameters=5;
+  Parameters=1;
 
   Executable = "/bin/sh";
   Arguments = "startpilot.sh";

diff --git a/examples/grid-sandbox/process_task.sh b/examples/grid-sandbox/process_task.sh
@@ -5,33 +5,36 @@
 # usage: ./process_task.sh [input] [tokenid]
 
 
-#Enable verbosity 
+# Enable verbosity 
 set -x
 
-#Obtain information for the Worker Node
+# GRID needs to find the CVMFS conda environment
+export PATH=/cvmfs/softdrive.nl/lodewijkn/miniconda3/bin:$PATH
+conda init bash
+source $HOME/.bashrc
+conda activate snakemake-picas
+
+# Obtain information for the Worker Node
 echo ""
 echo `date`
 echo ${HOSTNAME}
 
-#Initialize job arguments
+# Initialize job arguments
 INPUT=$1      
 TOKENID=$2
 OUTPUT=output_${TOKENID}
 echo $INPUT
 echo $TOKENID
 echo $OUTPUT
 
-#Start processing
+# Start processing
 eval $INPUT
 #./fractals -o $OUTPUT $INPUT
 if [[ "$?" != "0" ]]; then
     echo "Program interrupted. Exit now..."
     exit 1
 fi
 
-#Copy output to the grid storage
-#globus-url-copy file:///${PWD}/${OUTPUT} gsiftp://gridftp.grid.sara.nl:2811/pnfs/grid.sara.nl/data/lsgrid/homer/${OUTPUT}
-
 echo `date`
 
 exit 0
diff --git a/examples/snakemake.jdl b/examples/snakemake.jdl
@@ -0,0 +1,13 @@
+[
+  ParameterStart=0;
+  ParameterStep=1;
+  Parameters=1;
+
+  Executable = "/bin/sh";
+  Arguments = "startpilot.sh";
+  Stdoutput = "parametricjob.out";
+  StdError = "parametricjob.err";
+  InputSandbox = {"grid-sandbox/CouchDB-1.2.tar.gz", "grid-sandbox/picas.tar", "grid-sandbox/startpilot.sh", "local-example.py", "grid-sandbox/process_task.sh", "picasconfig.py", 
+                  "grid-sandbox/Snakefile", "grid-sandbox/plot-quals.py"};
+  OutputSandbox = {"parametricjob.out", "parametricjob.err"};
+]