{"__v":2,"_id":"562d4f7ae01a430d00c2c823","category":{"__v":5,"_id":"562d4dcc8c6e5a0d00d6ed1d","pages":["562d4df5e01a430d00c2c821","562d4f7ae01a430d00c2c823","562d514e54a5be0d00070b3d","562da6b1e01a430d00c2c873","562e652656486b0d00e3dc05"],"project":"5476bf0f817e8d080031f988","version":"5476bf10817e8d080031f98b","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2015-10-25T21:46:52.564Z","from_sync":false,"order":6,"slug":"command-line-interface","title":"Command-Line Interface"},"parentDoc":null,"project":"5476bf0f817e8d080031f988","user":"5476beec817e8d080031f986","version":{"__v":17,"_id":"5476bf10817e8d080031f98b","project":"5476bf0f817e8d080031f988","createdAt":"2014-11-27T06:05:04.263Z","releaseDate":"2014-11-27T06:05:04.263Z","categories":["5476bf10817e8d080031f98c","5477c46cf3736008009e9eb5","5477c474f3736008009e9eb6","5477c47ef3736008009e9eb7","5477c48ff3736008009e9eb8","5477c4948deb230800808bf0","54e68328154f8e0d0007b55c","54e90194c8e0c00d007ac061","54eed2275bf74a0d00ef4076","54f7a7be0a3cbb0d00d666fb","559b0ebf7ae7f80d0096d871","55d697f9ae529e0d00d34f03","562d4dcc8c6e5a0d00d6ed1d","562e591c4376430d006f17e0","568f0e73bdb9260d00149d8c","5719542aac1e2e0e001834c6","57a14a8ed778850e0047e230"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2015-10-25T21:54:02.673Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":1,"body":"[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Previewing Protocol Output\"\n}\n[/block]\nPreviewing a protocol supplies a script with parameters supplied in the \"preview\" section of a `manifest.json` file.  Read more about this below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/D0XhnOYTWymJhljbX6mQ_transcripticpreview.png\",\n        \"transcripticpreview.png\",\n        \"320\",\n        \"514\",\n        \"#6e9ecb\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Analyzing a Protocol\"\n}\n[/block]\nTo check whether your Autoprotocol is valid using Transcriptic's server-side checker, pipe any script that prints Autoprotocol to STDOUT to `transcriptic analyze`:\n```\n$ python my_protocol.py | transcriptic analyze\n✓ Protocol analyzed\n  2 instructions\n  1 container\n```\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/NkuP0VpQ0qiS3TCJHeeg_transcripticanalyze.png\",\n        \"transcripticanalyze.png\",\n        \"364\",\n        \"77\",\n        \"#98633f\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Launching a Run from a Protocol\"\n}\n[/block]\nSupply a project name or id to submit a run to:\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/b1IL2NsSsK4hJgqrfr8A_transcripticsubmit.png\",\n        \"transcripticsubmit.png\",\n        \"542\",\n        \"37\",\n        \"#74a4cc\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/GJouCCL3Snev4Q48NrZt_projectpage2.png\",\n        \"projectpage2.png\",\n        \"1425\",\n        \"410\",\n        \"#465d73\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Launching a Run in Test Mode\"\n}\n[/block]\nThe `--test` flag allows a run to be submitted in test mode, meaning it will never be executed\n\n```\n$ python my_protocol.py | transcriptic submit --project \"sequencing\" --title \"Sequencing run\" --test\n```\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Translating a Protocol to English\"\n}\n[/block]\nPipe any valid Autoprotocol to `transcriptic summarize` to get a summary of each step:\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/wpOlL32SQpia5SpG2cKg_transcripticsummarize.png\",\n        \"transcripticsummarize.png\",\n        \"377\",\n        \"121\",\n        \"#7ba7cd\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]","excerpt":"","slug":"the-basics","type":"basic","title":"Evaluating Protocols & Launching Runs"}

Evaluating Protocols & Launching Runs


[block:api-header] { "type": "basic", "title": "Previewing Protocol Output" } [/block] Previewing a protocol supplies a script with parameters supplied in the "preview" section of a `manifest.json` file. Read more about this below. [block:image] { "images": [ { "image": [ "https://files.readme.io/D0XhnOYTWymJhljbX6mQ_transcripticpreview.png", "transcripticpreview.png", "320", "514", "#6e9ecb", "" ] } ] } [/block] [block:api-header] { "type": "basic", "title": "Analyzing a Protocol" } [/block] To check whether your Autoprotocol is valid using Transcriptic's server-side checker, pipe any script that prints Autoprotocol to STDOUT to `transcriptic analyze`: ``` $ python my_protocol.py | transcriptic analyze ✓ Protocol analyzed 2 instructions 1 container ``` [block:image] { "images": [ { "image": [ "https://files.readme.io/NkuP0VpQ0qiS3TCJHeeg_transcripticanalyze.png", "transcripticanalyze.png", "364", "77", "#98633f", "" ] } ] } [/block] [block:api-header] { "type": "basic", "title": "Launching a Run from a Protocol" } [/block] Supply a project name or id to submit a run to: [block:image] { "images": [ { "image": [ "https://files.readme.io/b1IL2NsSsK4hJgqrfr8A_transcripticsubmit.png", "transcripticsubmit.png", "542", "37", "#74a4cc", "" ] } ] } [/block] [block:image] { "images": [ { "image": [ "https://files.readme.io/GJouCCL3Snev4Q48NrZt_projectpage2.png", "projectpage2.png", "1425", "410", "#465d73", "" ] } ] } [/block] [block:api-header] { "type": "basic", "title": "Launching a Run in Test Mode" } [/block] The `--test` flag allows a run to be submitted in test mode, meaning it will never be executed ``` $ python my_protocol.py | transcriptic submit --project "sequencing" --title "Sequencing run" --test ``` [block:api-header] { "type": "basic", "title": "Translating a Protocol to English" } [/block] Pipe any valid Autoprotocol to `transcriptic summarize` to get a summary of each step: [block:image] { "images": [ { "image": [ "https://files.readme.io/wpOlL32SQpia5SpG2cKg_transcripticsummarize.png", "transcripticsummarize.png", "377", "121", "#7ba7cd", "" ] } ] } [/block]