Example Command-Line Workflow
The command-line tool can be used to submit Autoprotocol to Strateos 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 Strateos 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
Updated over 2 years ago