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)