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