view fetch_organism_jbrowse.py @ 5:7610987e0c48 draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3

#!/usr/bin/env python
import os
import argparse
from webapollo import WAAuth, WebApolloInstance, GuessOrg, OrgOrGuess
import logging
import subprocess
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
    WAAuth(parser)
    OrgOrGuess(parser)
    parser.add_argument('target_dir', help='Target directory')

    args = parser.parse_args()

    wa = WebApolloInstance(args.apollo, args.username, args.password)
    # User must have an account
    org_cn = GuessOrg(args, wa)
    if isinstance(org_cn, list):
        org_cn = org_cn[0]
    org = wa.organisms.findOrganismByCn(org_cn)

    if not os.path.exists(args.target_dir):
        os.makedirs(args.target_dir)

    cmd = [
        'cp', '-R',
        org['directory'],
        os.path.join(args.target_dir, 'data')
    ]
    subprocess.check_call(cmd)