From 7d8770af1a1ad08fdaa9d83bde33e1e541969de2 Mon Sep 17 00:00:00 2001
From: Anthony Underwood <email2ants@gmail.com>
Date: Wed, 21 Apr 2021 16:39:55 +0100
Subject: [PATCH] Create sanger.config

---
 conf/sanger.config | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 conf/sanger.config

diff --git a/conf/sanger.config b/conf/sanger.config
new file mode 100644
index 0000000..686a3af
--- /dev/null
+++ b/conf/sanger.config
@@ -0,0 +1,26 @@
+params {
+  config_profile_description = 'The Wellcome Sanger Institute HPC cluster profile'
+  config_profile_contact = 'Anthony Underwood (@aunderwo)'
+  config_profile_url = 'https://www.sanger.ac.uk/group/informatics-support-group/'
+}
+
+singularity {
+  enabled = true
+  cacheDir   = "${baseDir}/singularity"
+  runOptions = '--bind /lustre --bind /nfs/pathnfs01 --bind /nfs/pathnfs02 --bind /nfs/pathnfs03 --bind /nfs/pathnfs04 --bind /nfs/pathnfs05 --bind /nfs/pathnfs06 --no-home'
+}
+
+process{
+  executor = 'lsf'
+  queue = 'normal'
+  errorStrategy = { task.attempt <= 5 ? "retry" : "finish" }
+  process.maxRetries = 5
+}
+
+executor{
+  name = 'lsf'
+  perJobMemLimit = true
+  poolSize = 4
+  submitRateLimit = '5 sec'
+  killBatchSize = 50
+}