def init(quiet=False, spark_conf=None, **kwargs):
""" Initialises hail context with variant-spark support.
:param kwargs: same as for hail.init()
"""
jars = [p.strip() for p in spark_conf.get("spark.jars", "").split(",")
] if spark_conf else []
vs_jar_path = vs.find_jar()
assert os.path.exists(vs_jar_path), "%s does not exist" % vs_jar_path
if not quiet:
sys.stderr.write("using variant-spark jar at '%s'\n" % vs_jar_path)
if not vs_jar_path in jars:
jars.append(vs_jar_path)
hl.init(quiet=quiet, spark_conf={'spark.jars': ",".join(jars)}, **kwargs)
def init(**kwargs):
jars = []
vs_jar_path=vs.find_jar()
assert os.path.exists(vs_jar_path), "%s does not exist" % vs_jar_path
sys.stderr.write("using variant-spark jar at '%s'\n" % vs_jar_path)
jars.append(vs_jar_path)
if pkg_resources.resource_exists(hl.__name__, "hail-all-spark.jar"):
hail_jar_path = pkg_resources.resource_filename(hl.__name__, "hail-all-spark.jar")
assert os.path.exists(hail_jar_path), "%s does not exist" % hail_jar_path
sys.stderr.write("using hail jar at '%s'\n" % hail_jar_path)
jars.append(hail_jar_path)
conf = SparkConf()
conf.set('spark.jars', ",".join(jars))
conf.set('spark.driver.extraClassPath', hail_jar_path)
conf.set('spark.executor.extraClassPath', './hail-all-spark.jar')
SparkContext._ensure_initialized(conf=conf)
hl.init(**kwargs)
def varspark_jar():
print(find_jar())
def varspark_submit():
args = ['spark-submit', '--jars', find_jar()] + sys.argv[1:]
exit(subprocess.call(" ".join(["'%s'" % arg for arg in args]), shell=True))