def run_job(self, job):
if not job.jar() or not os.path.exists(os.path.join(self.path,job.jar())):
logger.error("Can't find jar: {0}, full path {1}".format(job.jar(),
os.path.abspath(job.jar())))
raise Exception("job jar does not exist")
arglist = [JAVA] + job.java_opt() + ['-jar', os.path.join(self.path, job.jar())]
if job.main():
arglist.append(self._get_main(job))
if job.opts():
arglist += job.opts()
(tmp_files, job_args) = DefaultShellJobRunner._fix_paths(job)
arglist += job_args
cmd = ' '.join(arglist)
logger.info("\nJob runner '{0}';\n\trunning command '{1}'".format(self.__class__, cmd))
(stdout, stderr, returncode) = shell.exec_cmd(cmd, shell=True)
if returncode == 0:
logger.info("Shell job completed")
for a, b in tmp_files:
logger.info("renaming {0} to {1}".format(a.path, b.path))
# TODO : this should be relpath?
a.move(os.path.join(os.curdir, b.path))
# Some GATK programs generate bai or idx files on the fly...
if os.path.exists(a.path + ".bai"):
logger.info("Saw {} file".format(a.path + ".bai"))
os.rename(a.path + ".bai", b.path.replace(".bam", ".bai"))
if os.path.exists(a.path + ".idx"):
logger.info("Saw {} file".format(a.path + ".idx"))
os.rename(a.path + ".idx", b.path + ".idx")
else:
raise Exception("Job '{}' failed: \n{}".format(cmd, " ".join([stderr])))
def run_job(self, job):
if not job.exe():# or not os.path.exists(job.exe()):
logger.error("Can't find executable: {0}, full path {1}".format(job.exe(),
os.path.abspath(job.exe())))
raise Exception("executable does not exist")
arglist = [job.exe()]
if job.main():
arglist.append(self._get_main(job))
if job.opts():
arglist += job.opts()
# Need to call self.__class__ since fix_paths overridden in
# DefaultGzShellJobRunner
(tmp_files, job_args) = self.__class__._fix_paths(job)
arglist += job_args
cmd = ' '.join(arglist)
logger.info("\nJob runner '{0}';\n\trunning command '{1}'\n".format(self.__class__, cmd))
(stdout, stderr, returncode) = shell.exec_cmd(cmd, shell=True)
if returncode == 0:
logger.info("Shell job completed")
for a, b in tmp_files:
logger.info("renaming {0} to {1}".format(a.path, b.path))
# This is weird; using the example in luigi
# (a.move(b)) doesn't work, and using just b.path
# fails unless it contains a directory (e.g. './file'
# works, 'file' doesn't)
a.move(os.path.join(os.curdir, b.path))
else:
raise Exception("Job '{}' failed: \n{}".format(' '.join(arglist), " ".join([stderr])))
def run_job(self, job):
(arglist, tmp_files) = self._make_arglist(job)
(tmpdir, outdir) = tmp_files[0]
os.makedirs(os.path.join(os.curdir, tmpdir.path))
# Need to send output to temporary *directory*, not file
cmd = ' '.join(arglist)
logger.info("Job runner '{0}'; running command '{1}'".format(self.__class__, cmd))
(stdout, stderr, returncode) = shell.exec_cmd(cmd, shell=True)
if returncode == 0:
logger.info("Shell job completed")
for a, b in tmp_files:
logger.info("renaming {0} to {1}".format(a.path, b.path))
a.move(os.path.join(os.curdir, b.path))
else:
raise Exception("Job '{}' failed: \n{}".format(cmd.replace("= ", "="), " ".join([stderr])))
def run_job(self, job):
(arglist, tmp_files) = self._make_arglist(job)
if job.pipe:
return (arglist, tmp_files)
cmd = ' '.join(arglist)
logger.info("\nJob runner '{0}';\n\trunning command '{1}'\n".format(self.__class__, cmd))
(stdout, stderr, returncode) = shell.exec_cmd(cmd, shell=True)
if returncode == 0:
logger.info("Shell job completed")
for a, b in tmp_files:
logger.info("renaming {0} to {1}".format(a.path, b.path))
# This is weird; using the example in luigi
# (a.move(b)) doesn't work, and using just b.path
# fails unless it contains a directory (e.g. './file'
# works, 'file' doesn't)
a.move(os.path.join(os.curdir, b.path))
else:
raise Exception("Job '{}' failed: \n{}".format(' '.join(arglist), " ".join([stderr])))
def run_job(self, job):
(arglist, tmp_files) = self._make_arglist(job)
(tmpdir, outdir) = tmp_files[0]
os.makedirs(os.path.join(os.curdir, tmpdir.path))
# Need to send output to temporary *directory*, not file
cmd = ' '.join(arglist)
logger.info("Job runner '{0}'; running command '{1}'".format(
self.__class__, cmd))
(stdout, stderr, returncode) = shell.exec_cmd(cmd, shell=True)
if returncode == 0:
logger.info("Shell job completed")
for a, b in tmp_files:
logger.info("renaming {0} to {1}".format(a.path, b.path))
a.move(os.path.join(os.curdir, b.path))
else:
raise Exception("Job '{}' failed: \n{}".format(
cmd.replace("= ", "="), " ".join([stderr])))
def run_job(self, job):
(arglist, tmp_files) = self._make_arglist(job)
if job.pipe:
return (arglist, tmp_files)
cmd = ' '.join(arglist)
logger.info("\nJob runner '{0}';\n\trunning command '{1}'\n".format(
self.__class__, cmd))
(stdout, stderr, returncode) = shell.exec_cmd(cmd, shell=True)
if returncode == 0:
logger.info("Shell job completed")
for a, b in tmp_files:
logger.info("renaming {0} to {1}".format(a.path, b.path))
# This is weird; using the example in luigi
# (a.move(b)) doesn't work, and using just b.path
# fails unless it contains a directory (e.g. './file'
# works, 'file' doesn't)
a.move(os.path.join(os.curdir, b.path))
else:
raise Exception("Job '{}' failed: \n{}".format(
' '.join(arglist), " ".join([stderr])))
def run_job(self, job):
(arglist, tmp_files) = self._make_arglist(job)
cmd = ' '.join(arglist)
logger.info("\nJob runner '{0}';\n\trunning command '{1}'".format(self.__class__, cmd))
(stdout, stderr, returncode) = shell.exec_cmd(cmd, shell=True)
if returncode == 0:
logger.info("Shell job completed")
for a, b in tmp_files:
logger.info("renaming {0} to {1}".format(a.path, b.path))
# TODO : this should be relpath?
a.move(os.path.join(os.curdir, b.path))
# Some GATK programs generate bai or idx files on the fly...
if os.path.exists(a.path + ".bai"):
logger.info("Saw {} file".format(a.path + ".bai"))
os.rename(a.path + ".bai", b.path.replace(".bam", ".bai"))
if os.path.exists(a.path + ".idx"):
logger.info("Saw {} file".format(a.path + ".idx"))
os.rename(a.path + ".idx", b.path + ".idx")
else:
raise Exception("Job '{}' failed: \n{}".format(cmd, " ".join([stderr])))
def run_job(self, job):
(arglist, tmp_files) = self._make_arglist(job)
cmd = ' '.join(arglist)
logger.info("\nJob runner '{0}';\n\trunning command '{1}'".format(
self.__class__, cmd))
(stdout, stderr, returncode) = shell.exec_cmd(cmd, shell=True)
if returncode == 0:
logger.info("Shell job completed")
for a, b in tmp_files:
logger.info("renaming {0} to {1}".format(a.path, b.path))
# TODO : this should be relpath?
a.move(os.path.join(os.curdir, b.path))
# Some GATK programs generate bai or idx files on the fly...
if os.path.exists(a.path + ".bai"):
logger.info("Saw {} file".format(a.path + ".bai"))
os.rename(a.path + ".bai", b.path.replace(".bam", ".bai"))
if os.path.exists(a.path + ".idx"):
logger.info("Saw {} file".format(a.path + ".idx"))
os.rename(a.path + ".idx", b.path + ".idx")
else:
raise Exception("Job '{}' failed: \n{}".format(
cmd, " ".join([stderr])))
def run_job(self, job):
if not job.jar() or not os.path.exists(os.path.join(self.path,job.jar())):
logger.error("Can't find jar: {0}, full path {1}".format(job.jar(),
os.path.abspath(job.jar())))
raise Exception("job jar does not exist")
arglist = [JAVA] + job.java_opt() + ['-jar', os.path.join(self.path, job.jar())]
if job.main():
arglist.append(job.main())
if job.opts():
arglist += job.opts()
(tmp_files, job_args) = DefaultShellJobRunner._fix_paths(job)
arglist += job_args
cmd = ' '.join(arglist)
logger.info("\nJob runner '{0}';\n\trunning command '{1}'".format(self.__class__, cmd.replace("= ", "=")))
(stdout, stderr, returncode) = shell.exec_cmd(cmd.replace("= ", "="), shell=True)
if returncode == 0:
logger.info("Shell job completed")
for a, b in tmp_files:
logger.info("renaming {0} to {1}".format(a.path, b.path))
a.move(os.path.join(os.curdir, b.path))
else:
raise Exception("Job '{}' failed: \n{}".format(cmd.replace("= ", "="), " ".join([stderr])))