def register_nr_tasks(handler, params, databases): nr = databases['nr'] task = get_download_and_gunzip_task(nr['url'], nr['filename']) filename = path.join(handler.directory, nr['filename']) handler.register_task('download:nr', task, files={'nr': filename}) handler.register_task( 'lastdb:nr', LastDBTask().task(filename, filename, prot=True, params=params, task_dep=[task.name])) return handler
def register_uniref90_tasks(handler, params, databases): uniref90 = databases['uniref90'] task = get_download_and_gunzip_task(uniref90['url'], uniref90['filename']) filename = path.join(handler.directory, uniref90['filename']) handler.register_task('download:uniref90', task, files={'uniref90': filename}) handler.register_task( 'lastdb:uniref90', LastDBTask().task(filename, filename, prot=True, params=params, task_dep=[task.name])) return handler
def register_orthodb_tasks(handler, params, databases): orthodb = databases['OrthoDB'] archive_fn = '{0}.{1}'.format(orthodb['filename'], orthodb['fileformat']) target_fn = path.join(handler.directory, orthodb['filename']) dl_task = get_download_task(orthodb['url'], archive_fn, md5=orthodb['md5']) gz_task = get_gunzip_task(archive_fn, target_fn) handler.register_task('download:OrthoDB', dl_task, files={'OrthoDB-gz': archive_fn}) handler.register_task('gunzip:OrthoDB', gz_task, files={'OrthoDB': target_fn}) handler.register_task( 'lastdb:OrthoDB', LastDBTask().task(target_fn, target_fn, prot=True, params=params)) return handler