Commit fdfd9d95 authored by Fabrice Allain's avatar Fabrice Allain
Browse files

refactor: update cns script output with slurm

parent 8e50b10d
......@@ -96,7 +96,6 @@ class ClusteringXMLPickler(XMLBasePickler):
Returns
-------
"""
xml_elt = XMLElement(tag_order=ClusteringSettings.order)
......
......@@ -710,6 +710,17 @@ class PeakAssignerTextPickler(AriaBaseClass):
class PeakAssignerXMLPickler(XMLBasePickler):
def _xml_state(self, x):
"""
Define clustering xml tag from PeakAssignerSettings object
Parameters
----------
settings : PeakAssignerSettings object
Returns
-------
"""
e = XMLElement()
return e
......
......@@ -92,6 +92,8 @@ CSH_SCRIPT_REFINE = '''\
#BSUB -L %(sge_job_shell)s
#BSUB -oo refine.lsf.out
#BSUB -eo refine.lsf.err
#SBATCH -o refine.{sge_job_id}.slurm.out
#SBATCH -e refine.{sge_job_id}.slurm.err
#SBATCH -J %(sge_job_name)s
#SBATCH --ignore-pbs
......@@ -135,6 +137,8 @@ CSH_SCRIPT_CHECKPOINT = '''\
#BSUB -eo checkpoint.lsf.err
#SBATCH -J {sge_checkjob_name}
#SBATCH -d afterany:{sge_job_id}
#SBATCH -o checkpoint.{sge_job_id}.slurm.out
#SBATCH -e checkpoint.{sge_job_id}.slurm.err
#SBATCH --ignore-pbs
# CSH script which depends on refine.csh
......
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