def write_batch_script(self, n): """Instantiate and write the batch script to the work_dir.""" self.context['n'] = n self.context['queue'] = self.queue print self.context # first priority is batch_template if set if self.batch_template_file and not self.batch_template: # second priority is batch_template_file with open(self.batch_template_file) as f: self.batch_template = f.read() if not self.batch_template: # third (last) priority is default_template self.batch_template = self.default_template regex = re.compile(self.job_array_regexp) # print regex.search(self.batch_template) if not regex.search(self.batch_template): self.log.info("adding job array settings to batch script") firstline, rest = self.batch_template.split('\n',1) self.batch_template = u'\n'.join([firstline, self.job_array_template, rest]) regex = re.compile(self.queue_regexp) # print regex.search(self.batch_template) if self.queue and not regex.search(self.batch_template): self.log.info("adding PBS queue settings to batch script") firstline, rest = self.batch_template.split('\n',1) self.batch_template = u'\n'.join([firstline, self.queue_template, rest]) script_as_string = Itpl.itplns(self.batch_template, self.context) self.log.info('Writing instantiated batch script: %s' % self.batch_file) with open(self.batch_file, 'w') as f: f.write(script_as_string) os.chmod(self.batch_file, stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR)
def write_batch_script(self, n): """Instantiate and write the batch script to the work_dir.""" self.context['n'] = n script_as_string = Itpl.itplns(self.batch_template, self.context) log.msg('Writing instantiated batch script: %s' % self.batch_file) f = open(self.batch_file, 'w') f.write(script_as_string) f.close()
def write_batch_script(self, n): self.context['n'] = n template = open(self.template_file, 'r').read() log.msg('Using template for batch script: %s' % self.template_file) script_as_string = Itpl.itplns(template, self.context) log.msg('Writing instantiated batch script: %s' % self.batch_file) f = open(self.batch_file,'w') f.write(script_as_string) f.close()
def write_batch_script(self, n): self.context['n'] = n template = open(self.template_file, 'r').read() log.msg('Using template for batch script: %s' % self.template_file) script_as_string = Itpl.itplns(template, self.context) log.msg('Writing instantiated batch script: %s' % self.batch_file) f = open(self.batch_file, 'w') f.write(script_as_string) f.close()
def write_batch_script(self, n): """Instantiate and write the batch script to the work_dir.""" self.context['n'] = n self.context['queue'] = self.queue print self.context # first priority is batch_template if set if self.batch_template_file and not self.batch_template: # second priority is batch_template_file with open(self.batch_template_file) as f: self.batch_template = f.read() if not self.batch_template: # third (last) priority is default_template self.batch_template = self.default_template regex = re.compile(self.job_array_regexp) # print regex.search(self.batch_template) if not regex.search(self.batch_template): self.log.info("adding job array settings to batch script") firstline, rest = self.batch_template.split('\n', 1) self.batch_template = u'\n'.join( [firstline, self.job_array_template, rest]) regex = re.compile(self.queue_regexp) # print regex.search(self.batch_template) if self.queue and not regex.search(self.batch_template): self.log.info("adding PBS queue settings to batch script") firstline, rest = self.batch_template.split('\n', 1) self.batch_template = u'\n'.join( [firstline, self.queue_template, rest]) script_as_string = Itpl.itplns(self.batch_template, self.context) self.log.info('Writing instantiated batch script: %s' % self.batch_file) with open(self.batch_file, 'w') as f: f.write(script_as_string) os.chmod(self.batch_file, stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR)