Transcriptic

Example Command Line Workflow

The command-line tool can be used to submit Autoprotocol to Transcriptic to launch runs. To analyze some Autoprotocol JSON, you can simply copy it to your clipboard and run:

pbpaste | transcriptic analyze

It is also useful for submitting one-off scripts written using the Autoprotocol Python Library that print out their protocol, like:

import json
from autoprotocol.protocol import Protocol

p = Protocol()

bacterial_sample = p.ref("bacteria", None, "micro-1.5", discard=True)
test_plate = p.ref("test_plate", None, "96-flat", storage="cold_4")

p.dispense_full_plate(test_plate, "lb-broth-noAB", "50:microliter")
w = 0
amt = 1
while amt < 20:
  p.transfer(bacterial_sample.well(0), test_plate.well(w), "%d:microliter" % amt)
  amt += 2
  w +=1

print json.dumps(p.as_dict(), indent=2)

to view the JSON output of this script, simply run python my_script.py on the command line.

{
  "refs": {
    "bacteria": {
      "new": "micro-1.5", 
      "discard": true
    }, 
    "test_plate": {
      "new": "96-flat", 
      "store": {
        "where": "cold_4"
      }
    }
  }, 
  "instructions": [
    {
      "reagent": "lb-broth-noAB", 
      "object": "test_plate", 
      "columns": [
        {
          "column": 0, 
          "volume": "50:microliter"
        }, 
        {
          "column": 1, 
          "volume": "50:microliter"
        }, 
        {
          "column": 2, 
          "volume": "50:microliter"
        }, 
 ...

To analyze the output of this script and see how much it will cost to run:

$ python my_script.py | transcriptic analyze
  ✓ Protocol analyzed
  2 instructions
  2 containers
  $9.70

Then, to submit it and launch the run:

$ python my_script.py | transcriptic submit --project <project_id> --title "my cool run" 

After a run is submitted, it will be scheduled and executed on a workcell.

Your project's id can be found in its URL when viewing it on the Transcriptic website, or you can run transcriptic projects on the command line to see a list of your organization's projects, their titles and and their ids

Example Command Line Workflow


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