def load_jobs(self):
for m in self.models:
args = self.args.copy()
args["--model"] = m
job = Job(self.conf["app"]["phyml"], args,
parent_ids=[self.nodeid], jobname="phyml-bionj")
job.flag = "phyml"
self.jobs.append(job)
if self.lk_mode == "raxml":
raxml_args = {
"-f": "e",
"-s": self.alg_basename,
"-m": "PROTGAMMA%s" % m,
"-n": self.alg_basename+"."+m,
"-t": os.path.join(GLOBALS["tasks_dir"], job.jobid,
self.alg_basename+"_phyml_tree.txt")
}
raxml_job = Job(self.conf["app"]["raxml"], raxml_args,
parent_ids=[job.jobid], jobname="raxml-tree-optimize")
raxml_job.dependencies.add(job)
raxml_job.flag = "raxml"
raxml_job.model = m
self.jobs.append(raxml_job)
log.log(26, "Models to test %s", self.models)
def load_jobs(self):
conf = self.conf
for m in self.models:
args = self.args.copy()
args["--model"] = m
bionj_job = Job(conf["app"]["phyml"], args,
parent_ids=[self.nodeid])
bionj_job.jobname += "-bionj-" + m
bionj_job.jobcat = "bionj"
bionj_job.add_input_file(self.alg_phylip_file, bionj_job.jobdir)
self.jobs.append(bionj_job)
if self.lk_mode == "raxml":
raxml_args = {
"-f": "e",
"-s": pjoin(bionj_job.jobdir, self.alg_phylip_file),
"-m": "PROTGAMMA%s" % m,
"-n": self.alg_phylip_file+"."+m,
"-t": pjoin(bionj_job.jobdir,
self.alg_phylip_file+"_phyml_tree.txt")
}
raxml_job = Job(conf["app"]["raxml"], raxml_args,
parent_ids=[bionj_job.jobid])
raxml_job.jobname += "-lk-optimize"
raxml_job.dependencies.add(bionj_job)
raxml_job.model = m
raxml_job.jobcat = "raxml"
self.jobs.append(raxml_job)
def load_jobs(self):
for m in self.models:
args = self.args.copy()
args["--model"] = m
job = Job(self.conf["app"]["phyml"],
args,
parent_ids=[self.nodeid],
jobname="phyml-bionj")
job.flag = "phyml"
self.jobs.append(job)
if self.lk_mode == "raxml":
raxml_args = {
"-f":
"e",
"-s":
self.alg_basename,
"-m":
"PROTGAMMA%s" % m,
"-n":
self.alg_basename + "." + m,
"-t":
os.path.join(GLOBALS["tasks_dir"], job.jobid,
self.alg_basename + "_phyml_tree.txt")
}
raxml_job = Job(self.conf["app"]["raxml"],
raxml_args,
parent_ids=[job.jobid],
jobname="raxml-tree-optimize")
raxml_job.dependencies.add(job)
raxml_job.flag = "raxml"
raxml_job.model = m
self.jobs.append(raxml_job)
log.log(26, "Models to test %s", self.models)