add additional arguments to qsub; this addresses BIMSBbioinfo/pigx#8

BIMSBbioinfo · Mar 14, 2018 · 464de4f · 464de4f
1 parent a2efc74
commit 464de4f
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diff --git a/etc/settings.yaml.in b/etc/settings.yaml.in
@@ -14,6 +14,7 @@ execution:
     stack: 128M
     queue: all
     contact-email: none
+    args: ''    
   rules:
     __default__:
       threads: 1

diff --git a/pigx-rnaseq.in b/pigx-rnaseq.in
@@ -330,6 +330,8 @@ if config['execution']['submit-to-cluster']:
         else:
             raise
     qsub = "qsub -V -l h_stack={cluster.h_stack}  -l h_vmem={cluster.MEM} %s -b y -pe smp {cluster.nthreads} -cwd" % contact_email_string
+    if config['execution']['cluster']['args']:
+        qsub += " " + config['execution']['cluster']['args']
     command += [
         "--cluster-config={}".format(cluster_config_file),
         "--cluster={}".format(qsub),