0.11.0

• A recently introduced critical check_task permission error for runs longer than 5min is now fixed. In order to for this change to take effect, a tibanna unicorn must be redeployed - to overwrite an existing unicorn, it may need to be redeployed twice (due to an unknown AWS-related problem).

• Input bucket mounting support

  • The option can be set by specifying "mount": True for individual input file item. If "mount" is not specified or specified False, the file will be downloaded instead (as before).
  • The mount vs download option is set for individual file item and even if two or more files share the same bucket, one can choose one or the other for each file. Mounting reduces EBS volume size, whereas it is usually much faster to read a downloaded file.
  • For this to take effect, a tibanna unicorn must be redeployed.

• Environment variables can be passed for languages shell and snakemake.

  • They can be specified in the format of "input_env" : {"ENVNAME1": "1234", "ENVNAME2": "5678"} in the args field of the input execution json.
  • In the command, the environment variable should be used with double backslash (e.g. $NAME should be written as \\$NAME)