def java(items):
"""Check for presence of external Java 1.7 for tools that require it.
"""
if any([_needs_java(d) for d in items]):
min_version = "1.7"
max_version = "1.8"
with setpath.orig_paths():
java = utils.which("java")
if not java:
return (
"java not found on PATH. Java %s required for MuTect and GATK < 3.6."
% min_version)
p = subprocess.Popen([java, "-Xms250m", "-Xmx250m", "-version"],
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
output, _ = p.communicate()
p.stdout.close()
version = ""
for line in output.split("\n"):
if line.startswith(("java version", "openjdk version")):
version = line.strip().split()[-1]
if version.startswith('"'):
version = version[1:]
if version.endswith('"'):
version = version[:-1]
if (not version or LooseVersion(version) >= LooseVersion(max_version)
or LooseVersion(version) < LooseVersion(min_version)):
return (
"java version %s required for running MuTect and GATK < 3.6.\n"
"It needs to be first on your PATH so running 'java -version' give the correct version.\n"
"Found version %s at %s" % (min_version, version, java))
def java(items):
"""Check for presence of external Java 1.7 for tools that require it.
"""
if any([_needs_java(d) for d in items]):
min_version = "1.7"
max_version = "1.8"
with setpath.orig_paths():
java = utils.which("java")
if not java:
return ("java not found on PATH. Java %s required for MuTect and GATK < 3.6." % min_version)
p = subprocess.Popen([java, "-Xms250m", "-Xmx250m", "-version"],
stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
output, _ = p.communicate()
p.stdout.close()
version = ""
for line in output.split("\n"):
if line.startswith(("java version", "openjdk version")):
version = line.strip().split()[-1]
if version.startswith('"'):
version = version[1:]
if version.endswith('"'):
version = version[:-1]
if (not version or LooseVersion(version) >= LooseVersion(max_version) or
LooseVersion(version) < LooseVersion(min_version)):
return ("java version %s required for running MuTect and GATK < 3.6.\n"
"It needs to be first on your PATH so running 'java -version' give the correct version.\n"
"Found version %s at %s" % (min_version, version, java))
def run_mutect(self, params, tmp_dir=None):
with setpath.orig_paths():
with tx_tmpdir(self._config) as local_tmp_dir:
if tmp_dir is None:
tmp_dir = local_tmp_dir
cl = self.cl_mutect(params, tmp_dir)
prog = "MuTect"
do.run(cl, "MuTect: {0}".format(prog), None)
def run_mutect(self, params, tmp_dir=None):
with setpath.orig_paths():
with tx_tmpdir(self._config) as local_tmp_dir:
if tmp_dir is None:
tmp_dir = local_tmp_dir
cl = self.cl_mutect(params, tmp_dir)
prog = "MuTect"
do.run(cl, "MuTect: {0}".format(prog), None)