replace call() with run(). Factorize run_command() and run_docker_stack_deploy(service, working_dir)

replace call() with run(). Factorize run_command() and run_docker_stack_deploy(service, working_dir)

Move constants to file constants.py. Change config root to dict and update parse_config(). Change some config parameters name (galaxy_persist_data, tripal_banner_path, jbrowse_menu_url), update example config file and compose templates. Remove apollo config variables (webapollo_user, webapollo_password) in config file and in gspecies compose template, because apollo service not deployed here. Factorize parse_input() et parse_config(). Update description of scripts in main. Set default config file in scripts. Remove useless variable datasets_to_get in gga_get_data.py. Update README.md.

Remove unused imports. Factorize goto_species_dir(), create_galaxy_instance. Move constants at the beginning. Use upload_from_galaxy_fs() instead of upload_from_local(). Add get_bam_label()

Release 2.0

See merge request !8