def __init__(self, install_methods=None): if install_methods is None: install_methods = [] mafft_os = get_mafft_os() mafft_bitdepth = get_mafft_bitdepth() mafft_archive_extension = get_mafft_archive_extension(mafft_os) binaryPath = get_mafft_binary_path(mafft_os, mafft_bitdepth) binaryDir = get_mafft_binary_path(mafft_os, mafft_bitdepth, full=False) target_rel_path = '{binPath}'.format(binPath=binaryPath) verify_command = 'cd {dir}/mafft-{ver}/{bin_dir} && {dir}/mafft-{ver}/{binPath} --version > /dev/null 2>&1'.format( dir=util.file.get_build_path(), ver=TOOL_VERSION, binPath=binaryPath, bin_dir=binaryDir) destination_dir = '{dir}/mafft-{ver}'.format( dir=util.file.get_build_path(), ver=TOOL_VERSION) install_methods.append( tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION)) install_methods.append( tools.DownloadPackage( TOOL_URL.format(ver=TOOL_VERSION, os=mafft_os, ext=mafft_archive_extension), target_rel_path=target_rel_path, destination_dir=destination_dir, verifycmd=verify_command)) tools.Tool.__init__(self, 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.append(tools.CondaPackage(TOOL_NAME, executable=self.subtool_name, version=TOOL_VERSION)) install_methods.append(DownloadBmtagger(self.subtool_name)) tools.Tool.__init__(self, 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): unwanted = [ 'blast_formatter', 'blastdb_aliastool', 'blastdbcheck', 'blastdbcmd', 'convert2blastmask', 'deltablast', 'legacy_blast.pl', 'makembindex', 'makeprofiledb', 'psiblast', 'rpsblast', 'rpstblastn', 'segmasker', 'tblastn', 'tblastx', 'update_blastdb.pl', 'windowmasker' ] self.subtool_name = self.subtool_name if hasattr( self, "subtool_name") else "blastn" if install_methods is None: target_rel_path = 'ncbi-blast-2.2.29+/bin/' + self.subtool_name install_methods = [] install_methods.append( tools.CondaPackage(TOOL_NAME, executable=self.subtool_name, version=TOOL_VERSION)) install_methods.append( tools.DownloadPackage( get_url(), target_rel_path, post_download_command=' '.join( ['rm'] + ['ncbi-blast-2.2.29+/bin/' + f for f in unwanted]), post_download_ret=None)) #tools.Tool.__init__(self, install_methods=install_methods) super(BlastTools, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None): if install_methods is None: install_methods = [] install_methods.append( tools.CondaPackage(TOOL_NAME, version=CONDA_TOOL_VERSION)) muscle_os = get_muscle_os() if muscle_os != 'src': install_methods.append( tools.DownloadPackage( TOOL_URL.format(ver=TOOL_VERSION, os=muscle_os), 'muscle{}_{}'.format(TOOL_VERSION, muscle_os), verifycmd='{}/muscle{}_{} -version > /dev/null 2>&1'. format(util.file.get_build_path(), TOOL_VERSION, muscle_os))) # install_methods.append( # tools.DownloadPackage(TOOL_URL.format(ver=TOOL_VERSION, # os=muscle_os), # 'muscle{}/src/muscle'.format(TOOL_VERSION), # post_download_command='cd muscle{}/src; make -s'.format(TOOL_VERSION), # verifycmd='{}/muscle{}/src/muscle -version > /dev/null 2>&1'.format( # util.file.get_build_path(), TOOL_VERSION))) install_methods.append( tools.DownloadPackage( UNRELEASED_URL, 'muscle{}/src/muscle'.format(TOOL_VERSION), post_download_command='cd muscle{}/src; make -s'.format( TOOL_VERSION), verifycmd='{}/muscle{}/src/muscle -version > /dev/null 2>&1' .format(util.file.get_build_path(), TOOL_VERSION))) tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None): self.subtool_name = self.subtool_name if hasattr(self, "subtool_name") else None self.subtool_name_on_broad = self.subtool_name_on_broad if hasattr(self, "subtool_name_on_broad") else None if install_methods is None: install_methods = [] install_methods.append(tools.CondaPackage(TOOL_NAME, executable=self.subtool_name, version=TOOL_VERSION)) tools.Tool.__init__(self, install_methods=install_methods)
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, 'novoalign'), 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.CondaPackage(TOOL_NAME, executable="mummer", version=tool_version) ] tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None): if not install_methods: install_methods = [] install_methods.append( tools.CondaPackage(TOOL_NAME, version=CONDA_TOOL_VERSION, executable='ktImportTaxonomy')) super(Krona, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None): if install_methods is None: install_methods = [] install_methods.append( tools.CondaPackage(TOOL_NAME, executable="Trinity", version=CONDA_TOOL_VERSION)) tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None): if install_methods is None: install_methods = [ tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION, executable='Gap2Seq') ] 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.CondaPackage(TOOL_NAME, version=CONDA_TOOL_VERSION)) install_methods.append( DownloadAndBuildMuscleUnreleased(ver=TOOL_VERSION)) tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None): if install_methods is None: install_methods = [ tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION, executable='spades.py', verifycmd='spades.py --version') ] tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None, extra_genomes=None): extra_genomes = extra_genomes or ['KJ660346.2'] if not install_methods: install_methods = [] install_methods.append(tools.CondaPackage(TOOL_NAME, executable="snpEff", version=TOOL_VERSION)) install_methods.append(DownloadAndTweakSnpEff(URL, extra_genomes)) 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 = [] install_methods.append( tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION)) install_methods.append( DownloadGzipBinary(TOOL_URL.format(os=get_bintype()), 'tbl2asn')) tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None): self.subtool_name = self.subtool_name if hasattr(self, "subtool_name") else None if install_methods is None: install_methods = [] install_methods.append(tools.CondaPackage(TOOL_NAME, executable=self.subtool_name, version=TOOL_VERSION)) target_rel_path = 'picard-tools-{}/picard.jar'.format(TOOL_VERSION) install_methods.append(tools.DownloadPackage(TOOL_URL, target_rel_path, require_executability=False)) 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.CondaPackage(TOOL_NAME, version=TOOL_VERSION)) install_methods.append( tools.DownloadPackage(TOOL_URL, 'Trimmomatic-0.32/trimmomatic-0.32.jar', require_executability=False)) tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None): if not install_methods: install_methods = [] install_methods.append(tools.CondaPackage("jellyfish1", version=JELLYFISH_VERSION)) install_methods.append( DownloadAndInstallJellyfish( JELLYFISH_URL, os.path.join(JELLYFISH_DIR, 'bin', 'jellyfish') ) ) super().__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 = [] install_methods.append( tools.CondaPackage(TOOL_NAME, executable=self.subtool_name, version=TOOL_VERSION)) super(Kraken, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None): if install_methods is None: install_methods = [] install_methods.append( tools.CondaPackage(TOOL_NAME, executable="Trinity", version=CONDA_TOOL_VERSION)) install_methods.append( DownloadAndBuildTrinity(url, TRINITY_VERSION + '/Trinity.pl')) tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods=None): if not install_methods: install_methods = [] install_methods.append( tools.CondaPackage(TOOL_NAME, version=CONDA_TOOL_VERSION, executable='ktImportTaxonomy', patches=[('opt/krona/updateTaxonomy.sh', 'krona_updateTaxonomy.sh.patch') ])) super().__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 = [] install_methods.append( tools.CondaPackage('kraken', executable=self.subtool_name, version=KRAKEN_VERSION, channel='broad-viral')) super(Kraken, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None): unwanted = [ 'blast_formatter', 'blastdb_aliastool', 'blastdbcheck', 'blastdbcmd', 'convert2blastmask', 'deltablast', 'legacy_blast.pl', 'makembindex', 'makeprofiledb', 'psiblast', 'rpsblast', 'rpstblastn', 'segmasker', 'tblastn', 'tblastx', 'update_blastdb.pl', 'windowmasker' ] self.subtool_name = self.subtool_name if hasattr(self, "subtool_name") else "blastn" if install_methods is None: install_methods = [] install_methods.append(tools.CondaPackage(TOOL_NAME, executable=self.subtool_name, version=TOOL_VERSION)) super(BlastTools, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None): _log.debug("BWA_DIR: %s", BWA_DIR) if install_methods is None: install_methods = [] install_methods.append( tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION)) install_methods.append( tools.DownloadPackage( URL, os.path.join(BWA_DIR, 'bwa'), post_download_command="cd {}; make -s".format(BWA_DIR))) 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, install_methods = None): if install_methods is None: install_methods = [] os_type = self.get_os_type() binaryPath = self.get_selscan_binary_path( os_type ) target_rel_path = 'selscan-{ver}/{binPath}'.format(ver=TOOL_VERSION, binPath=binaryPath) verify_command = '{dir}/selscan-{ver}/{binPath} --help > /dev/null 2>&1'.format(dir=util.file.get_build_path(), ver=TOOL_VERSION, binPath=binaryPath) install_methods.append(tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION)) super(SelscanBaseTool, self).__init__(install_methods=install_methods)
def __init__(self, install_methods=None): if install_methods is None: install_methods = [ tools.CondaPackage(TOOL_NAME, version=tool_version), tools.DownloadPackage( url.format(ver=tool_version), 'MUMmer{}'.format(tool_version), post_download_command='cd MUMmer{}; make -s'.format( tool_version), verifycmd='{}/MUMmer{}/mummer -h > /dev/null 2>&1'.format( util.file.get_build_path(), tool_version)) ] 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.CondaPackage(TOOL_NAME, version=CONDA_TOOL_VERSION)) install_methods.append( tools.DownloadPackage( TOOL_URL, 'samtools-{}/samtools'.format(TOOL_VERSION), post_download_command='cd samtools-{}; make -s'.format( TOOL_VERSION ) ) ) 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.CondaPackage(TOOL_NAME, version=TOOL_VERSION, executable="gatk3")) install_methods.append( tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION, executable="gatk")) tools.Tool.__init__(self, install_methods=install_methods)
def __init__(self, install_methods = None): super(SelscanNormTool, self).__init__() if install_methods is None: install_methods = [] os_type = self.get_os_type() normBinaryPath = self.get_selscan_binary_path( os_type, binaryName="norm" ) target_norm_rel_path = 'selscan-{ver}/{binPath}'.format(ver=TOOL_VERSION, binPath=normBinaryPath) verify_norm_command = '{dir}/selscan-{ver}/{binPath} --help > /dev/null 2>&1'.format(dir=util.file.get_build_path(), ver=TOOL_VERSION, binPath=normBinaryPath) install_methods.append(tools.CondaPackage(TOOL_NAME, executable="norm", version=TOOL_VERSION)) tools.Tool.__init__(self, install_methods = install_methods)