def download_tool(tool,
tool_version,
required_files,
logger,
url,
only_clean=False):
tool_dirpath = get_dir_for_download(tool + tool_version,
tool,
required_files,
logger,
only_clean=only_clean)
if not tool_dirpath:
return None
if only_clean:
if os.path.isdir(tool_dirpath):
shutil.rmtree(tool_dirpath, ignore_errors=True)
return tool_dirpath
failed_compilation_flag = join(tool_dirpath, 'make.failed')
if not all(os.path.exists(join(tool_dirpath, fpath)) for fpath in required_files) and not \
check_prev_compilation_failed(tool, failed_compilation_flag):
downloaded_fpath = join(tool_dirpath, tool + '.tar.gz')
logger.main_info(' Downloading third-party tools...')
download_unpack_compressed_tar(tool, url, downloaded_fpath,
tool_dirpath, logger)
if not all(
os.path.exists(join(tool_dirpath, fpath))
for fpath in required_files):
logger.warning('Failed to download ' + tool + ' from ' + url +
'and unpack it into ' + tool_dirpath)
return None
return tool_dirpath
def download_db(logger, is_prokaryote, is_fungus=False, only_clean=False):
if is_prokaryote:
url = bacteria_db_url
clade = 'bacteria'
elif is_fungus:
url = fungi_db_url
clade = 'fungi'
else:
url = eukaryota_db_url
clade = 'eukaryota'
dirpath = get_dir_for_download('busco',
'Busco databases', [clade],
logger,
only_clean=only_clean)
if not dirpath:
return None
db_dirpath = join(dirpath, clade)
if only_clean:
if os.path.isdir(db_dirpath):
shutil.rmtree(db_dirpath, ignore_errors=True)
return True
if not os.path.exists(db_dirpath):
downloaded_fpath = join(dirpath, clade + '.tar.gz')
logger.main_info(' Downloading BUSCO database...')
download_unpack_compressed_tar(clade + ' database', url,
downloaded_fpath, db_dirpath, logger)
if not os.path.exists(db_dirpath):
logger.warning('Failed to download ' + clade + ' database from ' +
url + ' and unpack it into ' + dirpath)
return None
return db_dirpath
def download_db(logger, is_prokaryote, is_fungus=False, only_clean=False):
if is_prokaryote:
url = bacteria_db_url
clade = 'bacteria'
elif is_fungus:
url = fungi_db_url
clade = 'fungi'
else:
url = eukaryota_db_url
clade = 'eukaryota'
dirpath = get_dir_for_download('busco', 'Busco databases', [clade], logger, only_clean=only_clean)
if not dirpath:
return None
db_dirpath = join(dirpath, clade)
if only_clean:
if os.path.isdir(db_dirpath):
shutil.rmtree(db_dirpath, ignore_errors=True)
return True
if not os.path.exists(db_dirpath):
downloaded_fpath = join(dirpath, clade + '.tar.gz')
logger.main_info(' Downloading ' + clade + ' database...')
download_unpack_compressed_tar(clade + ' database', url, downloaded_fpath, db_dirpath, logger)
if not os.path.exists(db_dirpath):
logger.warning('Failed to download ' + clade + ' database from ' + url + 'and unpack it into ' + dirpath)
return None
return db_dirpath
def download_tool(tool, tool_version, required_files, logger, url, only_clean=False):
tool_dirpath = get_dir_for_download(tool + tool_version, tool, required_files, logger, only_clean=only_clean)
if not tool_dirpath:
return None
if only_clean:
if os.path.isdir(tool_dirpath):
shutil.rmtree(tool_dirpath, ignore_errors=True)
return tool_dirpath
failed_compilation_flag = join(tool_dirpath, 'make.failed')
if not all(os.path.exists(join(tool_dirpath, fpath)) for fpath in required_files) and not \
check_prev_compilation_failed(tool, failed_compilation_flag):
downloaded_fpath = join(tool_dirpath, tool + '.tar.gz')
logger.main_info(' Downloading ' + tool + '...')
download_unpack_compressed_tar(tool, url, downloaded_fpath, tool_dirpath, logger)
if not all(os.path.exists(join(tool_dirpath, fpath)) for fpath in required_files):
logger.warning('Failed to download ' + tool + ' from ' + url + 'and unpack it into ' + tool_dirpath)
return None
return tool_dirpath