additional qsub args

addresses BIMSBbioinfo/pigx#8
BIMSBbioinfo · Mar 14, 2018 · 8c464c1 · 8c464c1
1 parent b1cd1ce
commit 8c464c1
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diff --git a/etc/settings.yaml.in b/etc/settings.yaml.in
@@ -29,6 +29,7 @@ execution:
     missing-file-timeout: 120
     stack: 128M
     contact-email: none
+    args: ''
   rules:
     __default__:
       threads: 1

diff --git a/pigx-bsseq.in b/pigx-bsseq.in
@@ -488,6 +488,8 @@ if config['execution']['submit-to-cluster']:
         else:
             raise
     qsub = "qsub -V  %s -l h_stack={cluster.h_stack} -l h_vmem={cluster.MEM} %s -b y -pe smp {cluster.nthreads} -cwd" % ( queue_selection_string, contact_email_string)
+    if config['execution']['cluster']['args']:
+        qsub += " " + config['execution']['cluster']['args']
     command += [
         "--cluster-config={}".format(cluster_config_file),
         "--cluster={}".format(qsub),