Update readme with detailed procedure

README.md

@@ -12,26 +12,11 @@
 * [Running the Cluster Launcher](#running-the-cluster-launcher)
 * [Destroying the Clusters](#destroying-the-clusters)
 * [SeqWare Examples](#seqware-examples)
-    * [SeqWare - Single Node](#seqware---single-node)
-        * [Oozie Hadoop](#oozie-hadoop)
-        * [Oozie SGE](#oozie-sge)
-    * [SeqWare - Cluster](#seqware---cluster)
-        * [Oozie Hadoop](#oozie-hadoop-1)
-        * [Oozie SGE](#oozie-sge-1)
-    * [SeqWare - Install Only](#seqware---install-only)
-    * [SeqWare - CentOS](#seqware---centos)
-    * [SeqWare Query Engine - Single node](#seqware-query-engine---single-node)
-* [TCGA/ICGC PanCancer Examples](#tcgaicgc-pancancer-examples)
 * [Persistance of Ephemeral Disks - AWS](#persistance-of-ephemeral-disks---aws)
 * [Launching a single node instance from an AMI Image](#launching-a-single-node-instance-from-an-ami-image)
-* [OICR Examples](#oicr-examples)
-    * [General OICR Settings](#general-oicr-settings)
-    * [ICGC DCC Portal - Small Cluster](#icgc-dcc-portal---small-cluster)
-    * [ICGC DCC Portal - Large Cluster](#icgc-dcc-portal---large-cluster)
 * [Logging](#logging)
 * [Controlling the VM](#controlling-the-vm)
-    * [CentOS Information](#centos-information)
-        * [Veewee Installation and Usage Instructions (Mac)](#veewee-installation-and-usage-instructions-mac)
+* [CentOS Information](#centos-information)
 * [Debugging](#debugging)
 * [TODO](#todo)
 
@@ -375,6 +360,27 @@ The following templates exist for SeqWare-bag, they will be described in more
 detail in that repo's [README](https://github.com/SeqWare/seqware-bag):
 
 
+In brief, in order to use these projects together
+
+	mkdir working_dir
+	cd working_dir
+	git clone git@github.com:CloudBindle/Bindle.git
+	cd Bindle && git checkout 2.0-alpha.0
+	cd ..
+	git clone https://github.com/SeqWare/seqware-bag
+	cd seqware-bag && git checkout 1.0-alpha.0 
+	cd ../Bindle
+	cp ../seqware-bag/sample_configs/vagrant_cluster_launch.seqware.install.sge_cluster.json.template vagrant_cluster_launch.seqware.install.sge_cluster.json 
+        vim vagrant_cluster_launch.seqware.install.sge_cluster.json
+        perl bin/launcher/launch_cluster.pl --use-openstack --working-dir target --config-file vagrant_cluster_launch.seqware.install.sge_node.json
+        
+In order to re-run Ansible when doing development:
+
+        perl bin/launcher/launch_cluster.pl --use-openstack --working-dir target --config-file vagrant_cluster_launch.seqware.install.sge_node.json --run-ansible
+
+In order to run with pan-cancer modifications as well, please checkout and use the contents of [pancancer-bag](https://github.com/ICGC-TCGA-PanCancer/pancancer-bag) as well. 
+
+
 ## Persistance of Ephemeral Disks - AWS
 
 Amazon instances provisioned using Bindle store information such as file inputs and outputs, the /home directory, and the Oozie working directory in /mnt which is normally backed by ephemeral drives. If you wish them to persist (when rebooting instances or distributing images) you will need to mount them on an EBS volume instead. Follow the steps below to get an AMI image up and running with a single node instance!