Fix merge conflicts, still run update data release table if not stagi…

…ng but public

README.md

@@ -1,4 +1,5 @@
-![Docker Automated](https://img.shields.io/docker/automated/sagebionetworks/genie.svg) ![Docker Build](https://img.shields.io/docker/build/sagebionetworks/genie.svg)
+[![Docker Automated](https://img.shields.io/docker/automated/sagebionetworks/genie.svg)](https://hub.docker.com/r/sagebionetworks/genie) ![Docker Build](https://img.shields.io/docker/build/sagebionetworks/genie.svg)
+
 
 # AACR Project GENIE
 
@@ -26,40 +27,33 @@ genie validate -h
 genie validate clinical data_clincal_supp_SAGE.txt SAGE
 ```
 
-# SAGE USE ONLY
-## Processing instructions
-1. Go onto GENIE ec2
-
-2. Run shell script - `genie/processGENIE.sh` 
-
-**Releases**
-
-a. release 1.1.0 - 2.0.0
-```
-python database_to_staging.py Jan-2017 ~/cbioportal/ 1.1.0 --skipMutationsInCis
-python consortium_to_public.py Jul-2017 ~/cbioportal/ 2.0.0
+# SAGE BIONETWORKS USE ONLY
+## Batch Processing instructions
+1. Check docker hub builds to see if theres any failures
+2. Log into AWS Batch
+3. Run `genie-job-mainprocess`
+4. Run `genie-job-mafprocess` (Make sure to add `--createdMafDatabase` flag)
+5. Run `genie-job-vcfprocess`
+6. Run `genie-job-release` (Make sure to update release version and number)
+
+## Processing on EC2
+
+1. Input to database: `python input_to_database.py -h`
+2. Create GENIE Files
+**Example Releases**
+a. release 4.1-consortium and 4.0-public
 ```
-b. release 2.1.0 - 3.0.0
-```
-python database_to_staging.py Jul-2017 ~/cbioportal/ 2.1.0
-python consortium_to_public.py Jan-2018 ~/cbioportal/ 3.0.0
-```
-c. release 4.1-consortium and 4.0-public
-```
-python database_to_staging.py Jan-2018 ~/cbioportal/ 4.1-consortium
+python database_to_staging.py Jan-2018 ~/cbioportal/ 4.1-consortium --skipMutationsInCis
 python consortium_to_public.py Jul-2018 ~/cbioportal/ 4.0-public
 ```
-d. release 5.1-consortium and 5.0-public
+b. release 5.1-consortium and 5.0-public
 ```
 python database_to_staging.py Jul-2018 ~/cbioportal/ 5.1-consortium
 python consortium_to_public.py Jan-2019 ~/cbioportal/ 5.0-public
 ```
 
-3. Run dashboard scripts and check dashboard page to make sure numbers are correct
-
-4. If numbers don't match up, please check the log files to make sure no errors came up during processing.
 
-## Instructions for batch
+## Instructions to setup batch
 1. Build an AMI that can run batch jobs! Start from [this page](https://console.aws.amazon.com/batch/home?region=us-east-1#/first-run) and follow instructions and specify your docker image.  It is important at this stage that you time the building of your AMI, or your AMI will not be able to start batch jobs.  After doing so, you will have to start an instance with the AMI and run these 2 commands:
 
 ```
@@ -72,9 +66,8 @@ sudo rm -rf /var/lib/ecs/data/ecs_agent_data.json
 ## Adding GENIE sites
 
 1. Invite users to GENIE participant Team 
-2. Run python utility_sage/addCenter.py https://github.com/Sage-Bionetworks/Genie/blob/master/utility_sage/addCenter.py 
-* Creates CENTER (input/staging) folder (Set up ACLs) 
-* Update Center Mapping table https://www.synapse.org/#!Synapse:syn10061452/tables/
-* Add center to distribution tables: https://www.synapse.org/#!Synapse:syn10627220/tables/, https://www.synapse.org/#!Synapse:syn7268822/tables/
+2. Creates CENTER (input/staging) folder (Set up ACLs) 
+3. Update Center Mapping table https://www.synapse.org/#!Synapse:syn10061452/tables/
+4. Add center to distribution tables: https://www.synapse.org/#!Synapse:syn10627220/tables/, https://www.synapse.org/#!Synapse:syn7268822/tables/
 3. Add users to their GENIE folder