From ca4cd858b8c380221ab7fbac378cd4fff6a7ad6c Mon Sep 17 00:00:00 2001
From: Sheean Haley <haleysh@h2.carbonate.uits.iu.edu>
Date: Fri, 21 Aug 2020 11:54:38 -0400
Subject: [PATCH 1/2] pbs yaml

---
 cluster-pbs.yaml | 82 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100644 cluster-pbs.yaml

diff --git a/cluster-pbs.yaml b/cluster-pbs.yaml
new file mode 100644
index 0000000..f17d337
--- /dev/null
+++ b/cluster-pbs.yaml
@@ -0,0 +1,82 @@
+__default__:
+  account: haleysh 
+  command_options:
+    slurm:
+      account: --account={}
+      command: sbatch --parsable --qos=unlim
+      key_mapping: null
+      mem: --mem={}gb
+      name: --job-name={}
+      nodes: -N {}
+      queue: --partition={}
+      threads: -n {}
+      time: --time={}
+    pbs: 
+      command: sbatch
+      key_mapping: null
+      mem: -l vmem={}gb
+      name: -N {}
+      nodes: -l nodes={}
+      queue: –partition={}
+      threads: -l ppn={} 
+      time: -l walltime={}
+  cpupertask: 18
+  mem: 180
+  nodes: 1
+  queue: scavenger
+  system: slurm
+  tasks: 1
+  time: 1400
+fastqc:
+  account: haleysh
+  cpupertask: 5
+  mem: 1
+  queue: scavenger
+  tasks: 1
+  time: 720
+fastqc_trimmed:
+  account: haleysh
+  cpupertask: 5
+  mem: 1
+  queue: scavenger
+  tasks: 1
+  time: 720
+required:
+  accountname: haleysh
+  defaultqueue: scavenger
+  maxcores: 1
+  maxcpuspertask: 18
+  maxmemory: 180
+  maxtasks: 1
+transabyssmerge:
+  account: haleysh
+  cpupertask: 18
+  mem: 180
+  nodes: 1
+  queue: scavenger
+  tasks: 1
+  time: 10000
+trimmomatic:
+  account: haleysh
+  cpupertask: 5
+  mem: 48
+  nodes: 1
+  queue: scavenger
+  tasks: 1
+  time: 1400
+trinity:
+  account: haleysh
+  cpupertask: 20
+  mem: 500
+  nodes: 1
+  queue: bigmem 
+  tasks: 1
+  time: 10000
+velvet:
+  account: haleysh
+  cpupertask: 18
+  mem: 180
+  nodes: 1
+  queue: scavenger
+  tasks: 1
+  time: 10000

From 84ce07643f49264b4442d65d7ed77899d4cb56ad Mon Sep 17 00:00:00 2001
From: halexand <harriet.xander@gmail.com>
Date: Fri, 21 Aug 2020 11:58:12 -0400
Subject: [PATCH 2/2] updated pbs submit

---
 snake-submit-pbs.sh | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 snake-submit-pbs.sh

diff --git a/snake-submit-pbs.sh b/snake-submit-pbs.sh
new file mode 100644
index 0000000..a04173f
--- /dev/null
+++ b/snake-submit-pbs.sh
@@ -0,0 +1,2 @@
+snakemake --rerun-incomplete --jobs 50 --use-conda --cluster-config cluster-pbs.yaml --cluster "qsub -N {rule}.{wildcards} -l vmem={cluster.mem}gb,walltime={cluster.time},nodes={cluster.nodes}:ppn={cluster.cpupertask}"
+