def _gatk4_cmd(jvm_opts, params, data):
"""Retrieve unified command for GATK4, using 'gatk'. GATK3 is 'gatk3'.
"""
gatk_cmd = utils.which(os.path.join(os.path.dirname(os.path.realpath(sys.executable)), "gatk"))
return "%s && export PATH=%s:\"$PATH\" && gatk --java-options '%s' %s" % \
(utils.clear_java_home(), utils.get_java_binpath(gatk_cmd),
" ".join(jvm_opts), " ".join([str(x) for x in params]))
def run(self, subcmd, opts, memscale=None):
jvm_opts = get_picard_opts(self._config, memscale=memscale)
cmd = ["export", "PATH=%s:$PATH" % utils.get_java_binpath(), "&&"] + \
[self._cmd] + jvm_opts + [subcmd] + ["%s=%s" % (x, y) for x, y in opts] + \
["VALIDATION_STRINGENCY=SILENT"]
do.run(utils.clear_java_home() + " && " + " ".join(cmd),
"Picard: %s" % subcmd)
def _gatk4_cmd(jvm_opts, params, data):
"""Retrieve unified command for GATK4, using 'gatk'. GATK3 is 'gatk3'.
"""
gatk_cmd = utils.which(os.path.join(os.path.dirname(os.path.realpath(sys.executable)), "gatk"))
return "%s && export PATH=%s:\"$PATH\" && gatk --java-options '%s' %s" % \
(utils.clear_java_home(), utils.get_java_binpath(gatk_cmd),
" ".join(jvm_opts), " ".join([str(x) for x in params]))
def gatk_cmd(name, jvm_opts, params, config=None):
"""Retrieve PATH to gatk using locally installed java.
"""
if name == "gatk":
if isinstance(config, dict) and "config" not in config:
data = {"config": config}
else:
data = config
if not data or "gatk4" not in dd.get_tools_off(data):
return _gatk4_cmd(jvm_opts, params, data)
gatk_cmd = utils.which(
os.path.join(os.path.dirname(os.path.realpath(sys.executable)), name))
# if we can't find via the local executable, fallback to being in the path
if not gatk_cmd:
gatk_cmd = utils.which(name)
if gatk_cmd:
return "%s && export PATH=%s:$PATH && %s %s %s" % \
(utils.clear_java_home(), utils.get_java_binpath(gatk_cmd), gatk_cmd,
" ".join(jvm_opts), " ".join([str(x) for x in params]))
def gatk_cmd(name, jvm_opts, params, config=None):
"""Retrieve PATH to gatk using locally installed java.
"""
if name == "gatk":
if isinstance(config, dict) and "config" not in config:
data = {"config": config}
else:
data = config
if not data or "gatk4" not in dd.get_tools_off(data):
return _gatk4_cmd(jvm_opts, params, data)
else:
name = "gatk3"
gatk_cmd = utils.which(os.path.join(os.path.dirname(os.path.realpath(sys.executable)), name))
# if we can't find via the local executable, fallback to being in the path
if not gatk_cmd:
gatk_cmd = utils.which(name)
if gatk_cmd:
return "%s && export PATH=%s:\"$PATH\" && %s %s %s" % \
(utils.clear_java_home(), utils.get_java_binpath(gatk_cmd), gatk_cmd,
" ".join(jvm_opts), " ".join([str(x) for x in params]))
def run(self, subcmd, opts, memscale=None):
jvm_opts = get_picard_opts(self._config, memscale=memscale)
cmd = ["export", "PATH=%s:\"$PATH\"" % utils.get_java_binpath(), "&&"] + \
[self._cmd] + jvm_opts + [subcmd] + ["%s=%s" % (x, y) for x, y in opts] + \
["VALIDATION_STRINGENCY=SILENT"]
do.run(utils.clear_java_home() + " && " + " ".join(cmd), "Picard: %s" % subcmd)
