diff --git a/README.md b/README.md index e2a78488d3dc1f4e605f593253697c28588a2909..89c1c3cd52f14a398baf62fe41ae581da9dfedb9 100644 --- a/README.md +++ b/README.md @@ -30,6 +30,10 @@ To Run: * `--deriva` active **credential.json** file from [deriva-auth](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Uploading-files-via-Deriva-client-tools#from-a-remote-server) * `--bdbag` active **cookies.txt** file from [deriva-auth](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Uploading-files-via-Deriva-client-tools#from-a-remote-server) * `--repRID` mRNA-seq replicate RID + * `--source` consortium server source + * **dev** = [dev.gudmap.org](dev.gudmap.org) (default, does not contain all data) + * **staging** = [staging.gudmap.org](staging.gudmap.org) (does not contain all data) + * **production** = [www.gudmap.org](www.gudmap.org) (***does contain all data***) * `--refMoVersion` mouse reference version ***(optional)*** * `--refHuVersion` human reference version ***(optional)*** * `--refERCCVersion` human reference version ***(optional)*** @@ -39,6 +43,9 @@ To Run: * reference version consists of Genome Reference Consortium version, patch release and GENCODE annotation release # (leaving the params blank will use the default version tied to the pipeline version) * *current mouse* **38.p6.vM22** = GRCm38.p6 with GENCODE annotation release M22 * *current human* **38.p6.v31** = GRCh38.p12 with GENCODE annotation release 31 +* Tracking parameters ([Tracking Site](http://bicf.pipeline.tracker.s3-website-us-east-1.amazonaws.com/)): + * `--ci` boolean (default = false) + * `--dev` boolean (default = false) FULL EXAMPLE: -------------