
Usage: yabish COMMAND [COMMAND_ARGUMENTS...] [OPTIONS...]

COMMAND is either a command (ex. ls, jobs, attach ex.) or the name of a Tool you want to run on a YABI server.

Yabish can be used mainly to run jobs on a YABI server by specifying the name of the tool and any arguments you might want to pass in to it on the command line.
For example, to run a blast using yabish:

    $ yabish blast -i myseqs.fa -p blastn -d nt

Additionally, you can use Yabish to get information about jobs you are running on the server and for filesystem operations on your Filesystem Backends by running Yabish commands detailed below.


Yabish commands:

    jobs [START_DATE] - list all the jobs of the current user on the server. The optional START_DATE (by default today) can be used to go back in history until a given date. Format of the date is YYYY-MM-DD.

    status WORKFLOW_ID - display status information about the YABI job identified by worfklow id WORKFLOW_ID.

    attach WORKFLOW_ID - attach yabish to a job running on the YABI server. Yabish will wait until the job finishes or you interrupt it by CTRL+C.

    ls [URI] - list the directories and files of your filesystem backends configured in YABI. The optional URI is the URI of a directory you would like to list.

    cp SRC [DEST] - copy a file from a filesystem backend to the local filesystem. SRC is the URI of the file on a filesystem backend. The optional DEST (by default working directory) is a local directory or filename you want the SRC to be copied to.

    rm URI - remove a file from a filesystem backend. SRC is the URI of the file you would like to delete.

    backends - list the execution backends which you have access to in YABI.

    login USERNAME PASSWORD - login into Yabi with USERNAME/PASSWORD. This command is meant to be used only from automated scripts to avoid Yabish to prompt for the username and password

    logout - logout a user from Yabi.


Environment variables:

  YABISH_YABI_URL : set to the URL of the YABI server you would like Yabish to run your remote commands on (ex. https://ccg.murdoch.edu.au/yabi)

Options:
  --yabi-bg            Run the yabish remote job in the background
  --backend BACKEND    Sets the execution backend. Use "yabish backends" to list backends.
  --yabi-url YABI_URL  The URL of the YABI server (ex. https://ccg.murdoch.edu.au/yabi). Alternatively, you can set this by the YABISH_YABI_URL environment variable
  --yabi-debug         Run in debug mode - used by developers only to test yabish
