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): 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 = [] 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 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): _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, 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, install_methods=None): if install_methods is None: install_methods = [] install_methods.append(tools.CondaPackage(TOOL_NAME, executable="prinseq-lite.pl", version=TOOL_VERSION)) target_rel_path = 'prinseq-lite-{ver}/prinseq-lite.pl'.format(ver=TOOL_VERSION) install_methods.append( tools.DownloadPackage( TOOL_URL, target_rel_path, post_download_command='chmod +x {}'.format(target_rel_path), require_executability=True ) ) tools.Tool.__init__(self, install_methods=install_methods)