From 84ef8119cb293873ea95aa76c114bfb0f1f98ba2 Mon Sep 17 00:00:00 2001
From: mbychkovskiy <mikhail.bychkovskiy@quantori.com>
Date: Mon, 16 May 2022 11:46:38 +0400
Subject: [PATCH] Update links to Anfisa example datasets

---
 README.md | 42 ++++++++++++++++++++++++++++++------------
 deploy.sh |  4 ++--
 2 files changed, 32 insertions(+), 14 deletions(-)

diff --git a/README.md b/README.md
index 4e9927d4..8e47d5da 100644
--- a/README.md
+++ b/README.md
@@ -2,15 +2,17 @@
 
 <!-- toc -->
 
-- [Overview](#overview)
-- [Online Development Documentation](#online-development-documentation)
-- [Public Demo](#public-demo)
-- [Installation](#installation)
-  * [Select branch or release:](#select-branch-or-release)
-  * [Installation instructions](#installation-instructions)
-    + [Installing via Docker](#installing-via-docker)
-    + [Installing without Docker](#installing-without-docker)
-  * [Ingesting demo whole genome](#ingesting-demo-whole-genome)
+- [Anfisa](#anfisa)
+  - [Overview](#overview)
+  - [Online Development Documentation](#online-development-documentation)
+  - [Public Demo](#public-demo)
+  - [Installation](#installation)
+    - [Select branch or release:](#select-branch-or-release)
+    - [Installation instructions](#installation-instructions)
+      - [Installing via Docker](#installing-via-docker)
+      - [Installing without Docker](#installing-without-docker)
+    - [Ingesting demo whole genome](#ingesting-demo-whole-genome)
+  - [Public Demo](#public-demo-1)
 
 <!-- tocstop -->
 
@@ -291,6 +293,22 @@ The port is configurable in your configuration file. Configuration file is locat
 Here are sample commands that can be executed:
 
     curl -L -O https://forome-dataset-public.s3.us-south.cloud-object-storage.appdomain.cloud/pgp3140_wgs_nist-v4.2.tar.gz
-    docker cp pgp3140_wgs_nist-v4.2.tar.gz anfisa7:/anfisa/a-setup/data/examples/
-    docker exec -it anfisa7 sh -c 'cd /anfisa/a-setup/data/examples && tar -zxvf pgp3140_wgs_nist-v4.2.tar.gz'
-    docker exec -it anfisa7 sh -c 'PYTHONPATH=/anfisa/anfisa/ python3 -u -m app.storage -c /anfisa/anfisa.json -m create --reportlines 1000 -f -k xl -i /anfisa/a-setup/data/examples/pgp3140_wgs_nist-v4.2/pgp3140_wgs_nist-v4.2.cfg XL_PGP3140_NIST_V42'
+
+    docker cp pgp3140_wgs_nist-v4.2.tar.gz anfisa-backend:/anfisa/a-setup/data/examples/
+    docker exec -it anfisa-backend sh -c 'cd /anfisa/a-setup/data/examples && tar -zxvf pgp3140_wgs_nist-v4.2.tar.gz'
+    docker exec -it anfisa-backend sh -c 'PYTHONPATH=/anfisa/anfisa/ python3 -u -m app.storage -c /anfisa/anfisa.json -m create --reportlines 1000 -f -k xl -i /anfisa/a-setup/data/examples/pgp3140_wgs_nist-v4.2/pgp3140_wgs_nist-v4.2.cfg XL_PGP3140_NIST_V42'
+
+## Public Demo 
+
+For a quick introduction, look at a demo of Anfisa based on a high 
+confidence small variants callset v 4.2 created by NIST 
+by integrating results of sequencing, alignment and 
+variant calling from different sources; including 
+both short and long read techniques.  
+
+
+The demo server with REST API and a stable built-in UI 
+is available at: https://api.demo.forome.org/
+
+A novel [React](https://reactjs.org/) Front End is under development
+and a beta version can be previewed at: https://app.demo.forome.org/ 
diff --git a/deploy.sh b/deploy.sh
index 2a023a4e..0d7d85f0 100755
--- a/deploy.sh
+++ b/deploy.sh
@@ -3,7 +3,7 @@
 usage()
 {
 cat << EOF
-	Usage: $0 --workdir=/path/to/workdir/for/anfisa/0.7/ 
+	Usage: $0 --workdir=/path/to/workdir/for/anfisa/0.7/
 EOF
 }
 
@@ -11,7 +11,7 @@ EOF
 for flag in "$@"
 do
 	case $flag in
-		--workdir=*) 
+		--workdir=*)
 			WORKDIR=${flag#*=}
 			echo WORKDIR=$WORKDIR
 			if [[ $WORKDIR != /* ]]; then