From f3e1ea296e6f320d85c0d514a1325cf5f8b6d7cb Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 14 Jul 2020 22:35:27 -0500
Subject: [PATCH] Update README.md
---
README.md | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/README.md b/README.md
index e2a7848..89c1c3c 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:
-------------
--
GitLab