def __init__(self, path=None, license_path=None):
self.tool_version = None
install_methods = []
for novopath in [path, os.environ.get('NOVOALIGN_PATH')]:
if novopath is not None:
install_methods.append(
tools.PrexistingUnixCommand(os.path.join(
novopath, TOOL_NAME),
require_executability=True))
install_methods.append(
tools.PrexistingUnixCommand(shutil.which(TOOL_NAME),
require_executability=True))
post_verify_command = None
for novo_license_path in [
license_path,
os.environ.get("NOVOALIGN_LICENSE_PATH"), ''
]:
if novo_license_path is not None and os.path.isfile(
novo_license_path):
# called relative to the conda bin/ directory
uname = os.uname()
# we ideally want the "update" copy operation
# but only GNU cp has it. On OSX, the license will be copied each time.
if uname[0] == 'Darwin':
copy_operation = ''
else:
copy_operation = '-u'
post_verify_command = "cp {copy_operation} {lic_path} ./".format(
copy_operation=copy_operation, lic_path=novo_license_path)
break # if we've found a license file, stop looking
#install_methods.append(tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION, post_verify_command=post_verify_command))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = [
tools.PrexistingUnixCommand(shutil.which(TOOL_NAME),
verifycmd='tbl2asn --help')
]
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if not install_methods:
install_methods = []
install_methods.append(
tools.PrexistingUnixCommand(shutil.which('kraken2'),
require_executability=False))
super(Kraken2, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = [
tools.PrexistingUnixCommand(shutil.which(TOOL_NAME),
require_executability=True)
]
super(MafftTool, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
path = _get_vphaser2_path()
install_methods = []
install_methods.append(tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION))
install_methods.append(tools.PrexistingUnixCommand(path))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None, extra_genomes=None):
self.jvmMemDefault = '4g'
if not install_methods:
install_methods = [tools.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]
self.known_dbs = set()
self.installed_dbs = set()
super(SnpEff, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = [
tools.PrexistingUnixCommand(shutil.which('cd-hit'),
require_executability=True)
]
super(CdHit, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = [
tools.PrexistingUnixCommand(shutil.which(TOOL_NAME),
require_executability=False)
]
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, path=None):
self.tool_version = None
install_methods = []
for jarpath in [path, os.environ.get('GATK_PATH')]:
if jarpath:
if not jarpath.endswith('.jar'):
jarpath = os.path.join(jarpath, 'GenomeAnalysisTK.jar')
install_methods.append(
tools.PrexistingUnixCommand(
jarpath,
verifycmd='java -jar %s --version &> /dev/null' %
jarpath,
verifycode=0,
require_executability=False))
install_methods.append(
tools.PrexistingUnixCommand(shutil.which(TOOL_NAME),
require_executability=True))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, path=None):
self.tool_version = None
install_methods = []
for novopath in [path, os.environ.get('NOVOALIGN_PATH'), '']:
if novopath is not None:
install_methods.append(
tools.PrexistingUnixCommand(os.path.join(
novopath, 'novoalign'),
require_executability=True))
install_methods.append(
tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION))
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, path=None):
self.tool_version = None
for megan_path in [path, os.environ.get('MEGAN_PATH')]:
if not megan_path:
continue
if os.path.isdir(megan_path):
megan_path = os.path.join(megan_path, 'MEGAN')
install_methods = [
tools.PrexistingUnixCommand(
megan_path,
verifycmd='{} -h > /dev/null'.format(megan_path),
verifycode=0,
require_executability=True)
]
self.license_file = os.environ.get('MEGAN_LICENSE_PATH')
self.data_dir = os.environ.get('MEGAN_DATA_PATH')
super(Megan, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
if not install_methods:
install_methods = [
tools.PrexistingUnixCommand(shutil.which('ktImportTaxonomy'))
]
super(Krona, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
if not install_methods:
install_methods = [
tools.PrexistingUnixCommand(shutil.which('diamond'))
]
super(Diamond, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
self.subtool_name = self.subtool_name if hasattr(self, "subtool_name") else "kraken"
if not install_methods:
install_methods = [tools.PrexistingUnixCommand(shutil.which(self.subtool_name), require_executability=False)]
super(Kraken, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None):
self.subtool_name = self.subtool_name if hasattr(self, "subtool_name") else "bmtagger.sh"
if install_methods is None:
install_methods = []
install_methods = [tools.PrexistingUnixCommand(shutil.which(self.subtool_name), require_executability=False)]
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = [
tools.PrexistingUnixCommand(shutil.which(TOOL_NAME))
]
tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None):
if install_methods is None:
install_methods = []
install_methods.append(tools.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True))
super(Minimap2, self).__init__(install_methods=install_methods)
