https://github.com/mskcc/pipeline-kickoff
https://github.com/mskcc/pipeline-kickoff
Last synced: 11 months ago
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- Host: GitHub
- URL: https://github.com/mskcc/pipeline-kickoff
- Owner: mskcc
- Created: 2017-07-07T18:27:34.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2022-03-09T18:59:32.000Z (over 4 years ago)
- Last Synced: 2025-02-28T08:28:47.864Z (over 1 year ago)
- Language: Java
- Size: 1.13 MB
- Stars: 1
- Watchers: 10
- Forks: 0
- Open Issues: 7
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Metadata Files:
- Readme: README.md
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README
# pipeline-kickoff
http://plvpipetrack1.mskcc.org:8099/display/PipelineInitiation/Analysis+Pipeline+Initiation+Home
Pipeline kickoff gathers information from LIMS (using LIMS API) and file system and creates manifest files which are used by analysis pipeline.
This code is run as a cron job retrieving recently delivered requests for which those files can be generated.
### Latest Versions
The latest release version is `1.1.9` for `BIC`, `1.25.2` for `ROSLIN`.
**NOTE**
* Code base was inherited from `BIC` and needs refactoring and better test coverage.
* The combination of `BIC` and `ROSLIN` is in branch [`SAP-296-combine-bic-and-roslin-branch`](https://github.com/mskcc/pipeline-kickoff/tree/SAP-296-combine-bic-and-roslin-branch), which combines bic (`tag: v1.1.9-bic`) and rolsin (`tag: v1.25.2-roslin`) branch.
### Arguments
* `-p, PROJECT_ID`. e.g. `-p 12345_A`
* `-e`. run as exome
* `-f`. force generation of files even when there are errors