Merge branch 'release/1.1.2-java8'

Author: SolomonShorser-OICR

Dockerfile

@@ -1,6 +1,6 @@
-# SeqWare 
+# SeqWare
 #
-# VERSION               1.1.0-alpha.6 
+# VERSION               1.1.2
 #
 # Setup SeqWare with WhiteStar (no sge, no oozie, no metadata)
 # Volume mount \datastore to persist the contents of your workflows
@@ -31,10 +31,10 @@ WORKDIR /home/seqware
 USER seqware
 # setup seqware white star
 RUN git clone https://github.com/SeqWare/seqware-bag.git
-WORKDIR /home/seqware/seqware-bag 
-RUN git checkout 1.0-beta.0
+WORKDIR /home/seqware/seqware-bag
+RUN git checkout 1.0.1
 ADD inventory /etc/ansible/hosts
-RUN ansible-playbook mini-seqware-install.yml -c local --extra-vars "seqware_version=1.1.1"
+RUN ansible-playbook mini-seqware-install.yml -c local --extra-vars "seqware_version=1.1.2"
 ENV PATH /home/seqware/bin:/tmp/ansible/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 # at this point, seqware has been fully setup
 USER root

README.md

@@ -1,33 +1,43 @@
+[![](https://badge.imagelayers.io/seqware/seqware_whitestar:latest.svg)](https://imagelayers.io/?images=seqware/seqware_full:latest 'Get your own badge on imagelayers.io')
+
 ## Users - running the container
 
+These steps take place in a temporary directory that you create for playing around with this container.
+
 1. Set permissions on datastore which will hold results of workflows after they run
 
         mkdir workflows && mkdir datastore
         chmod a+wrx workflows && chmod a+wrx datastore
 
-2. Run container and login with the following (while persisting workflow run directories to datastore). 
- 
-        docker run --rm -h master -t -v `pwd`/datastore:/datastore  -i seqware/seqware_whitestar:1.1.1
+The workflows directory can be used later to store additional workflows that you wish to run. Datastore will contain the results of your workflow. This tutorial will use the HelloWorld workflow which is pre-built into the container and does not need to be installed in /datastore .
+
+2. Run container and login with the following (while persisting workflow run directories to datastore).
 
-3. You should now be inside the running container. Run the HelloWorld (sample) workflow with 
+        docker run --rm -h master -t -v `pwd`/datastore:/datastore  -i seqware/seqware_whitestar:1.1.2-java8
+
+3. You should now be inside the running container. Run the HelloWorld (sample) workflow with
+
+        seqware bundle launch --dir ~/provisioned-bundles/Workflow_Bundle_HelloWorld_1.0-SNAPSHOT_SeqWare_1.1.2-java8/ --no-metadata
 
-        seqware bundle launch --dir ~/provisioned-bundles/Workflow_Bundle_HelloWorld_1.0-SNAPSHOT_SeqWare_1.1.1/ --no-metadata
-        
 4. Exit the container
 
         exit
 
 5. Note that you can also run commands or workflows programmatically rather than interactively.
 
-        docker run --rm -h master -t -v `pwd`/datastore:/mnt/datastore -i seqware/seqware_whitestar:1.1.1 seqware bundle launch --dir /home/seqware/provisioned-bundles/Workflow_Bundle_HelloWorld_1.0-SNAPSHOT_SeqWare_1.1.1/ --no-metadata
+        docker run --rm -h master -t -v `pwd`/datastore:/mnt/datastore -i seqware/seqware_whitestar:1.1.2-java8 seqware bundle launch --dir /home/seqware/provisioned-bundles/Workflow_Bundle_HelloWorld_1.0-SNAPSHOT_SeqWare_1.1.2-java8/ --no-metadata
 
 6. Note that the Docker client is installed in the container so you can connect the client with the host's Docker daemon in order to run workflows that use Docker calls
 
-        docker run -h master --rm -t -i -v /var/run/docker.sock:/var/run/docker.sock seqware/seqware_whitestar:1.1.1
+        docker run -h master --rm -t -i -v /var/run/docker.sock:/var/run/docker.sock seqware/seqware_whitestar:1.1.2-java8
         docker run -t -i ubuntu /bin/bash
 
+**NOTE:** There are two versions of seqware/seqware_whitestar version "1.1.2":
+  - seqware/seqware_whitestar:1.1.2 which contains Java 6.
+  - seqware/seqware_whitestar:1.1.2-java8 which contains Java 8.
+
 ## Developers - building the image locally
 
-1. Assuming docker is installed properly, build image with 
+1. Assuming docker is installed properly, build image with
 
-        docker build  -t seqware/seqware_whitestar:1.1.1 . 
+        docker build  -t seqware/seqware_whitestar:1.1.2-java8 .