Merge branch 'release/0.1.1'

Author: SolomonShorser-OICR

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changes
 
+## 0.1.1
+ - Added the begining of an OpenStack-specific config document.
+ - Fixed incorrect consonance version number in mustache file.
+
 ## 0.1.0
  - Major changes:
   - Support for non-Amazon clouds environments:

OpenStack_setup.md

@@ -0,0 +1,20 @@
+# PanCancer CLI on OpenStack
+
+This document will cover some of the differences you may notice when running the launcher on OpenStack
+
+## Initial questions
+
+The installer script will ask OpenStack-specific questions when you run the PanCancer launcher on OpenStack. These questions will ask you about:
+
+ - Your OpenStack username. This should be formatted as `<tenant>:<username>`. For example: `sweng:bob` should be entered if your username is `bob` for the `sweng` tenant.
+ - Your OpenStack password.
+ - The URL for your OpenStack endpoint. It will probably look something like this:  http://10.5.73.21:5000/v2.0
+ - The OpenStack Region in which the launcher should be running.
+ - The Security Group for your launcher.
+ - The Network ID of the network that the launcher will be running in.
+ - The OpenStack Zone. This is optional.
+ 
+## Running the Generator
+
+When you run the generator, you may be prompted to enter the name of an OpenStack workflow configuration name.
+This is because it is possible for different OpenStack environments to use different configurations for the same workflow. Variations might be the base imaged ID and flavour. 

QuickStart.md

@@ -99,7 +99,7 @@ $ scp -i <YOUR PEM KEY FILE>.pem <YOUR PEM KEY FILE>.pem ubuntu@<YOUR VM PUBLIC
 ### Run Installer
 Download & execute the [bootstrap script](scripts/install_bootstrap) like this:
 ```
-$ wget -qO install_bootstrap https://github.com/ICGC-TCGA-PanCancer/cli/releases/download/0.1.0/install_bootstrap && bash install_bootstrap
+$ wget -qO install_bootstrap https://github.com/ICGC-TCGA-PanCancer/cli/releases/download/0.1.1/install_bootstrap && bash install_bootstrap
 ```
 This script will install docker (you can skip this step by answering "N" if you already have docker installed), the pancancer_launcher image, and collect some basic configuration info to get the launcher started. 
 
@@ -121,7 +121,7 @@ bash install_bootstrap
 
 If you follow the directions above you will find yourself dropped into the docker container that has all our launcher tools. The prompt will look something like this (the hostname, "f27e86874dfb" in this case, and possibly the version number, will be different):
 
-    [LAUNCHER 3.2.0] ubuntu@f27e86874dfb:~/arch3$
+    [LAUNCHER 3.2.1] ubuntu@f27e86874dfb:~/arch3$
 
 
 ###Running workflows

scripts/install_bootstrap

@@ -1,7 +1,7 @@
 #! /bin/bash
 set -e
-PANCANCER_LAUNCHER_VERSION=3.2.0
-PANCANCER_CLI_VERSION=0.1.0
+PANCANCER_LAUNCHER_VERSION=3.2.1
+PANCANCER_CLI_VERSION=0.1.1
 WORKFLOW_LISTING_URL=https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/cli/${PANCANCER_CLI_VERSION}/config/workflowlist.json
 
 cat <<MSG
@@ -12,11 +12,11 @@ the PanCancer donors.  This launcher host can then launch one or more worker VMs
 workflows installed on them for processing one or more genomes specified by the user.
 
 This system requires the following:
-* Docker support in your Linux distribution (Ubuntu 14.04 is officially supported by the Pancancer Launcher)
-* AWS credentials
+* Docker support in your Linux distribution (Ub1untu 14.04 is officially supported by the Pancancer Launcher).
+* AWS credentials, if you are using Amazon EC2.
 * A GNOS key (or keys) which are used to both download Docker images for our workflows, dependencies, as well as data from from GNOS servers used in the project.
   Please ensure that these files are in ~/.gnos
-* Alternatively (or in addition to) the GNOS keys, a token for downloading workflows, dependencies, as well as donor data files from S3
+* Alternatively (or in addition to) the GNOS keys, a token for downloading workflows, dependencies, as well as donor data files from S3.
 MSG
 
 # Ask the user a question and save the answer.

scripts/pancancer_config.mustache

@@ -68,7 +68,7 @@
     "queueName": "pancancer_arch_3",
     "lvm_device_whitelist": "{{lvm_devices}}",
     "single_node_lvm": true,
-    "pancancer_arch3_version": "1.1-rc.3",
+    "pancancer_arch3_version": "1.1-rc.2",
     "seqware_engine":"whitestar-parallel",
     "seqware_use_custom_settings":false,
     "azure":{{use_azure}},