From cfe13fe6c1b72bbfeb27d56843c93f7714cc505d Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Mon, 15 Mar 2021 15:42:30 +0000
Subject: [PATCH] Fixed typo & added singularity tmpdir

---
 conf/eddie.config    | 44 +++++++++++++++++++++++++-------------------
 nfcore_custom.config |  2 +-
 2 files changed, 26 insertions(+), 20 deletions(-)

diff --git a/conf/eddie.config b/conf/eddie.config
index 3968783..6145908 100644
--- a/conf/eddie.config
+++ b/conf/eddie.config
@@ -5,39 +5,45 @@ params {
   config_profile_url = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing'
 }
 
-conda {
-  createTimeout = '2h'
-}
-
-singularity {
-  enabled = true
+executor {
+  name = "sge"
+  queueSize = "100"
 }
 
 process {
-  executor = 'sge'
-
-  // memory environment & options
-  clusterOptions = {"-l h_vmem=${task.memory.bytes/task.cpus}"}
-  penv = 'sharedmem'
+  clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes/task.cpus}" : null }
+  scratch = true
+  penv = { task.cpus > 1 ? "sharedmem" : null }
 
   // common SGE error statuses
-  errorStrategy = {task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish'}
+  errorStrategy = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'}
   maxErrors = '-1'
   maxRetries = 3
 
-  // load module script for Anaconda and Singularity
-  beforeScript = { '. /etc/profile.d/modules.sh; sleep 2; ' }
-  module = 'anaconda/5.3.1'
-  module = 'singularity/3.5.3'
+  beforeScript =
+  """
+  '. /etc/profile.d/modules.sh
+  sleep 2
+  module load 'anaconda/5.3.1'
+  module load 'roslin/singularity/3.5.3'
+  export SINGULARITY_TMPDIR="\$TMPDIR"
+  """
 }
 
 params {
   saveReference = true
-
   // iGenomes reference base
-  igenomes_base = '/exports/igmm/eddie/NextGenResources/igenomes/'
-
+  igenomes_base = '/exports/igmm/eddie/NextGenResources/igenomes'
   max_memory = 384.GB
   max_cpus = 32
   max_time = 240.h
 }
+
+env {
+  MALLOC_ARENA_MAX=1
+}
+
+singularity {
+  envWhitelist = "SINGULARITY_TMPDIR"
+  runOptions = '-p'
+}
\ No newline at end of file
diff --git a/nfcore_custom.config b/nfcore_custom.config
index 7abbb7e..b338f1c 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -23,7 +23,7 @@ profiles {
   crick        { includeConfig "${params.custom_config_base}/conf/crick.config" }
   czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
   ebc          { includeConfig "${params.custom_config_base}/conf/ebc.config" }
-  eddie	       { includeConfig "${params.custom_config_bsae}/conf/eddie.config" }
+  eddie	       { includeConfig "${params.custom_config_base}/conf/eddie.config" }
   icr_davros   { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
   imperial     { includeConfig "${params.custom_config_base}/conf/imperial.config" }
   imperial_mb  { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }