Update README.md

README.md

@@ -36,6 +36,8 @@ You should see the command lines correponding to each workflow rule coming up on
 If using a cluster, the call is slightly different :
 ~~~
 source activate microSysMics
+# The following awk command just set absolute filepaths in the test manifest file. To run only once.
+awk -v P="$(pwd)" 'BEGIN{FS=",";}NR==1{print $1","$2","$3;}NR>1{print $1","P"/"$2","$3;}' test/manifest.csv > test/manifest.tmp && mv test/manifest.tmp test/manifest.csv
 snakemake -p --use-conda --latency-wait 60 --cluster "qsub" --jobs 40 --jobscript microSysMics.sh
 ~~~