📝 document distributed cluster execution

project/bin/README.md

@@ -0,0 +1,18 @@
+# Computerome2 (CR2) scripts
+
+Cluster exectuion script for CR2 using a torque-pbs queue.
+
+
+## Distributed
+
+```bash
+qsub run_snakemake_cluster.sh -N snakemake_exp -v configfile=config/single_dev_dataset/example/config.yaml,prefix=exp
+```
+
+## Single node
+
+```bash
+qsub run_snakemake.sh -N grid_exp
+```
+
+

project/bin/run_snakemake.sh

@@ -5,8 +5,8 @@
 ### Job name (comment out the next line to get the name of the script used as the job name)
 #PBS -N  sn_grid
 ### Output files (comment out the next 2 lines to get the job name used instead)
-#PBS -e qsub_logs${PBS_JOBNAME}.${PBS_JOBID}.e
-#PBS -o qsub_logs${PBS_JOBNAME}.${PBS_JOBID}.o
+#PBS -e qsub_logs/${PBS_JOBNAME}.${PBS_JOBID}.e
+#PBS -o qsub_logs/${PBS_JOBNAME}.${PBS_JOBID}.o
 ### Email notification: a=aborts, b=begins, e=ends, n=no notifications
 #PBS -m ae -M [email protected]
 ### Number of nodes

project/workflow/bin/README.md

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+# Scripts for pbs-torque cluster execution
+
+We ran the software partly on a pbs-torque cluster
+
+`qsub-status_v2.py` is used by snakemake to  query the status of a submitted job in case the job,
+in case the job is not ran locally within the main process running snakemake.
+
+`create_qsub_commands.py` is a script which create some job submission commands.
+
+`jobscript.sh` is a script which sets up conda before the subcommand create from within
+a snakemake job is run.
+
+
+> None of this is needed in case snakemake is non-distributed on a single node.