Software Engineers

Please visit this page once you have done things necessary here: https://mskcc.github.io/on-boarding/

• The best place to start would be to understand the data flow:

  • LIMS/SMILE -> Voyager -> JUNO

• Learn more about the codebases listed below that form Voyager

• Learn about the codebases the form mPATH

Sites

Code/Project Management

Resource	URL
ACCESS/Voyager team uses this to manage sprints/stories. In addition, ACCESS uses this to keep track of the statuses of samples.	clickup.com
Auto Track Sample Status	jira.mskcc.org:8090
Internal Gitlab where MPath and other software is hosted.	http://crux.mskcc.org:8929/mpath http://crux.mskcc.org:8929/access (forked from mpath repositories)
Code specific to ACCESS team pipelines.	github.com/mskcc-access
Code for other CMO/MSK teams	github.com/mskcc
Information on HPC/LSF	https://mskcchpc.org/
Beagle	https://github.com/mskcc/beagle
Hermes	https://github.com/mskcc/hermes
Ridgeback	https://github.com/mskcc/ridgeback

Applications

Application	URL
LIMS	For Authentication ask your Manager: https://igolims.mskcc.org:8443/LimsRest/swagger-ui.html
Beagle API	http://silo:4001 (Staging) http://voyager:5001 (Production)
Ridgeback API	http://silo:4003 (Staging) http://voyager:5003 (Production)
Flower (Celery Task UI) for Voyager, for Production only	http://voyager:4001
ELK for Voyager	bic-dockerapp01.mskcc.org:5601/
MPath (for Clinical)	https://mpath.mskcc.org/
MPath (for Research)	http://access01:7331/api/ui/
CVR (to be replaced by MPath)	cvr.mskcc.org:8083/

People

Projects, who to speak with, slack channel

• MPath & CVR (Aijazuddin Syed/Anoop Balakrishnan Rema)
• Voyager Projects [Beagle/Seqosystem/Ridgeback] (Sinisa Ivkovic/Nikhil Kumar/Allan Bolipata)

  • #voyager

• LIMS (David Mcmanamon)
• MDB (Angelica Ochoa/Benjamin Gross/Allan Bolipata)

  • #metadb-informatics

• Toil/CWL (Nikhil Kumar)

• ACCESS (Ronak Shah)

  • #msk-access

• ACCESS Servers (HPC Request/Neeraj Paramasivam)