def _picard_version(config, jar_file):
if jar_file not in _PICARD_VERSION_CACHE:
params = AtomicJavaCmdBuilder(jar_file,
temp_root=config.temp_root,
jre_options=config.jre_options)
params.add_value("--version")
name = "Picard " + os.path.basename(jar_file)
requirement = versions.Requirement(call=params.finalized_call,
name=name,
search=r"^(\d+)\.(\d+)",
checks=versions.GE(1, 82))
_PICARD_VERSION_CACHE[jar_file] = requirement
return _PICARD_VERSION_CACHE[jar_file]
def _picard_version(config, jar_file):
if jar_file not in _PICARD_VERSION_CACHE:
params = AtomicJavaCmdBuilder(jar_file,
temp_root=config.temp_root,
jre_options=config.jre_options)
params.add_value("--version")
name = "Picard " + os.path.basename(jar_file)
requirement = versions.Requirement(call=params.finalized_call,
name=name,
search=r"^(\d+)\.(\d+)",
checks=versions.GE(1, 82))
_PICARD_VERSION_CACHE[jar_file] = requirement
return _PICARD_VERSION_CACHE[jar_file]
def _get_gatk_version_check(config):
"""Returns a version-check object for the "GenomeAnalysisTK.jar" located at
config.jar_root; for now, this check only serves to verify that the JAR can
be executed, which may not be the case if the JRE is outdated.
"""
jar_file = os.path.join(config.jar_root, "GenomeAnalysisTK.jar")
if jar_file not in _GATK_VERSION:
params = AtomicJavaCmdBuilder(jar_file, temp_root=config.temp_root, jre_options=config.jre_options)
params.add_value("--version")
# Any version is fine; for now just catch old JREs
requirement = versions.Requirement(
call=params.finalized_call, name="GenomeAnalysisTK", search=r"^(\d+)\.(\d+)", checks=versions.Any()
)
_GATK_VERSION[jar_file] = requirement
return _GATK_VERSION[jar_file]
def _get_gatk_version_check(config):
"""Returns a version-check object for the "GenomeAnalysisTK.jar" located at
config.jar_root; for now, this check only serves to verify that the JAR can
be executed, which may not be the case if the JRE is outdated.
"""
jar_file = os.path.join(config.jar_root, "GenomeAnalysisTK.jar")
if jar_file not in _GATK_VERSION:
params = AtomicJavaCmdBuilder(jar_file,
temp_root=config.temp_root,
jre_options=config.jre_options)
params.add_value("--version")
# Any version is fine; for now just catch old JREs
requirement = versions.Requirement(call=params.finalized_call,
name="GenomeAnalysisTK",
search=r"^(\d+)\.(\d+)",
checks=versions.Any())
_GATK_VERSION[jar_file] = requirement
return _GATK_VERSION[jar_file]