From c849cb549b10358ea821b7b42278fa9f60ae15c0 Mon Sep 17 00:00:00 2001
From: Henry Webel <henry.webel@cpr.ku.dk>
Date: Wed, 8 Nov 2023 17:23:00 +0100
Subject: [PATCH] :memo: document distributed cluster execution

---
 project/bin/README.md          | 18 ++++++++++++++++++
 project/bin/run_snakemake.sh   |  4 ++--
 project/workflow/bin/README.md | 14 ++++++++++++++
 3 files changed, 34 insertions(+), 2 deletions(-)
 create mode 100644 project/bin/README.md
 create mode 100644 project/workflow/bin/README.md

diff --git a/project/bin/README.md b/project/bin/README.md
new file mode 100644
index 000000000..3e84a2791
--- /dev/null
+++ b/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
+```
+
+
diff --git a/project/bin/run_snakemake.sh b/project/bin/run_snakemake.sh
index e01a13255..9b7b2d032 100644
--- a/project/bin/run_snakemake.sh
+++ b/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 henry.webel@cpr.ku.dk
 ### Number of nodes
diff --git a/project/workflow/bin/README.md b/project/workflow/bin/README.md
new file mode 100644
index 000000000..a45c2b8a8
--- /dev/null
+++ b/project/workflow/bin/README.md
@@ -0,0 +1,14 @@
+# 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.
\ No newline at end of file