Commit 8d14ebd8 authored by Fabrice Allain's avatar Fabrice Allain
Browse files

fix: revision of output slurm file for cns refine.csh

parent fdfd9d95
......@@ -107,7 +107,7 @@ class ClusteringXMLPickler(XMLBasePickler):
def load_from_element(self, xml_elt):
"""
Load clustering settings from XMLElement
Instantiate clustering settings from XMLElement
Parameters
----------
......
......@@ -280,10 +280,15 @@ class Job(Thread, AriaBaseClass):
checkscript = '_%s' % str(jobid) if jobid else ''
if jobid:
# Update script output with job id
script = checkscript.join(os.path.splitext(d['script']))
self._up_script(d['script'], {'sge_job_id': jobid},
script)
# Create specific checkpoint file
checkscript = checkscript.join(os.path.splitext(d['check_script']))
self._up_script(d['check_script'], {'sge_job_id': jobid},
checkscript)
d['script'] = script
d['check_script'] = checkscript
checkcmd = self.checkcmd_template % d
......
......@@ -41,6 +41,8 @@ def peak_shape(deltas, errors):
class PeakAssignerSettings(Settings):
order = ()
def create(self):
from .Settings import NonNegativeFloat
from .Settings import YesNoChoice, FourLetterString, String
......@@ -711,7 +713,7 @@ class PeakAssignerTextPickler(AriaBaseClass):
class PeakAssignerXMLPickler(XMLBasePickler):
def _xml_state(self, x):
"""
Define clustering xml tag from PeakAssignerSettings object
Instantiate Peak assigner xml tag from PeakAssignerSettings object
Parameters
----------
......
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