Update, this is the current working implementation that supports consonance-wes.

install.yml

@@ -1,7 +1,6 @@
 ---
 # file: install.yml
 # This file is used for installing a container host
-
 # Not sure why, but I needed this to create a /etc/hosts that actually works with the Ubuntu image here on openstack
 - hosts: master:worker
   become: yes

roles/common/tasks/main.yml

@@ -10,14 +10,20 @@
   with_items:
     - python
 
-- name: Download get-pip
-  get_url: url=https://bootstrap.pypa.io/get-pip.py dest=/home/ubuntu/downloads/get-pip.py
+- name: Update ubuntu system
+  raw: sudo apt-get update
+
+#- name: Download get-pip
+#  get_url: url=https://bootstrap.pypa.io/get-pip.py dest=/home/ubuntu/downloads/get-pip.py
+- name: Install build pre-requisites
+  raw: sudo apt-get install -y build-essential libssl-dev libffi-dev python-dev
 
 - name: Install pip
   become: yes
   become_user: root
-  shell: python /home/ubuntu/downloads/get-pip.py
-
+  raw: apt-get install -y python-pip
+#shell: python /home/ubuntu/downloads/get-pip.py
+#TODO: provisioning fails in the following!
 - name: Install docker-py
   become: yes
   become_user: root
@@ -32,3 +38,13 @@
   become: yes
   become_user: root
   file: state=directory path=/home/ubuntu/.aws owner=ubuntu
+
+- name: Setup dockstore config directory
+  become: yes
+  become_user: root
+  file: state=directory path=/home/ubuntu/.dockstore owner=ubuntu
+
+- name: Setup dockstore config directory 2
+  become: yes
+  become_user: root
+  file: state=directory path=/root/.dockstore owner=ubuntu

roles/consonance/tasks/main.yml

@@ -1,6 +1,7 @@
 ---
-- name: Get Architecture3 jar file
-  get_url: url=https://www.dropbox.com/s/giy9ayxlvpoohiz/consonance-arch-2.0-alpha.11-SNAPSHOT.jar?dl=1 dest=/home/ubuntu/consonance-arch-{{ consonance_arch_version }}.jar
+- name: Get Architecture3 jar file # This needs to be updated to the latest release of consonance dependencies!
+  raw: sudo wget https://www.dropbox.com/s/p254pqswn3o53xg/consonance-arch-2.0.0-alpha.16-SNAPSHOT.jar -O /home/ubuntu/consonance-arch-{{ consonance_arch_version }}.jar
+  #https://www.dropbox.com/s/giy9ayxlvpoohiz/consonance-arch-2.0-alpha.11-SNAPSHOT.jar?dl=1 dest=/home/ubuntu/consonance-arch-{{ consonance_arch_version }}.jar
   #get_url: url=https://seqwaremaven.oicr.on.ca/artifactory/simple/seqware-release/io/consonance/consonance-arch/{{ consonance_arch_version }}/consonance-arch-{{ consonance_arch_version }}.jar dest=/home/ubuntu/consonance-arch-{{ consonance_arch_version }}.jar
 
 # The "endless" flag for the worker is not a true/false, it's "--endless" or "".
@@ -12,7 +13,7 @@
   set_fact: endless_worker_flag=""
   when: endless_worker is not defined or not endless_worker
 
-- name: Get kill-worker script
+- name: Get kill-worker scriptls
   template: src=kill_worker_daemon.j2 dest=/home/ubuntu/kill_worker_daemon.sh
 
 - name: Get run-worker script
@@ -37,62 +38,28 @@
   when: seqware_use_custom_settings is defined and seqware_use_custom_settings
 
 - name: Copy over keys/credentials for workers.
-  copy: src={{ item }} dest={{ item }} owner=ubuntu
+  copy: src={{ item }} dest=/root/.aws owner=root
   with_fileglob:
-    - /home/ubuntu/.gnos/*
-    - /home/ubuntu/.aws/*
+    - /root/.aws/*
+
+- name: Copy over dockstore credentials
+  copy: src={{ item }} dest=/root/.dockstore/ owner=root
+  with_fileglob:
+    - /root/.dockstore/*
+
+- name: Install setuptools
+  raw: sudo pip install setuptools==36.5.0
 
 - name: Install avro
-  pip: name=avro executable=pip2.7 version=1.8.1
+  raw: sudo pip install avro==1.8.1
 
 - name: Install schema-salad
-  pip: name=schema-salad executable=pip2.7 version=1.14.20160708181155
+  raw: sudo pip install schema-salad==2.6.20170806163416
 
 - name: Install cwltool
-  pip: name=cwltool executable=pip2.7 version=1.0.20160712154127
-
-- name: Copy over patched job files
-  copy: src=roles/consonance/files/job_new.py dest=/usr/local/lib/python2.7/dist-packages/cwltool/job.py owner=root
-
-- name: Copy over patched process files
-  copy: src=roles/consonance/files/process_new.py dest=/usr/local/lib/python2.7/dist-packages/cwltool/process.py owner=root
-
-- name: Copy over patched main files
-  copy: src=roles/consonance/files/main_new.py dest=/usr/local/lib/python2.7/dist-packages/cwltool/main.py owner=root
-
-- name: Delete compiled job files
-  command: rm -f /usr/local/lib/python2.7/dist-packages/cwltool/job.pyc
-
-- name: Delete compiled process files
-  command: rm -f /usr/local/lib/python2.7/dist-packages/cwltool/process.pyc
-
-- name: Delete compiled main files
-  command: rm -f /usr/local/lib/python2.7/dist-packages/cwltool/main.pyc
-
-# install dcc-storage
-
-#- name: Create required directory
-#  become_user: root
-#  file: path=/icgc/dcc-storage/ owner=ubuntu state=directory
-#
-#- name: Create working directory
-#  become_user: root
-#  file: path=/icgc/dcc-storage/archive owner=ubuntu state=directory
-#
-#- name: Get file
-#  get_url: url=https://seqwaremaven.oicr.on.ca/artifactory/dcc-release/org/icgc/dcc/dcc-storage-client/{{ dcc_storage_version }}/dcc-storage-client-{{ dcc_storage_version }}-dist.tar.gz dest=/icgc/dcc-storage/archive
-#
-#- name: Unarchive the dcc tool
-#  unarchive: src=/icgc/dcc-storage/archive/dcc-storage-client-{{ dcc_storage_version }}-dist.tar.gz dest=/icgc/dcc-storage/archive  copy=no
-#
-#- name: Copy files extracted files into correct location
-#  shell: creates=/icgc/dcc-storage/bin/dcc-storage-client mv /icgc/dcc-storage/archive/dcc-storage-client-{{ dcc_storage_version }}/* /icgc/dcc-storage/
-#
-#- name: Template shell script
-#  template: src=dcc-storage-client.j2 dest=/icgc/dcc-storage/bin/dcc-storage-client owner=ubuntu
+  raw: sudo pip install cwltool==1.0.20170217172322
 
 # end dcc-storage
-
 - name: Run worker as daemon
   become_user: root
   shell: chdir=/home/ubuntu nohup bash /home/ubuntu/run_worker_daemon.sh &

roles/containers/tasks/main.yml

@@ -19,11 +19,12 @@
   with_dict: s3_containers | default({})
   when: s3_containers is defined
 
-- name: Remove AWS config and credentials, now that objects have been downloaded.
-  file: path={{ item }} state=absent
-  when: s3_containers is defined
-  with_fileglob:
-    - /home/ubuntu/.aws/*
+#TODO: We do not want to get rid of the credentials so that aws can upload outputs
+#- name: Remove AWS config and credentials, now that objects have been downloaded.
+#  file: path={{ item }} state=absent
+#  when: s3_containers is defined
+#  with_fileglob:
+#    - /home/ubuntu/.aws/*
 
 - name: Load Private images
   shell: docker load -i /home/ubuntu/downloads/{{ item.value.name }}.tar

roles/workflow/tasks/main.yml

@@ -33,11 +33,12 @@
   retries: 5
   delay: 15
 
-- name: Remove AWS config, now that objects have been downloaded.
-  file: path={{ item }} state=absent
-  when: s3_containers is defined or s3_workflows is defined
-  with_fileglob:
-    - /home/ubuntu/.aws/*
+#TODO: Require docstore to upload outputs back to aws.
+#- name: Remove AWS config, now that objects have been downloaded.
+#  file: path={{ item }} state=absent
+#  when: s3_containers is defined or s3_workflows is defined
+#  with_fileglob:
+#    - /home/ubuntu/.aws/*
 
 # TODO: Some of these plays are copy-pasted (ugh!) with different hashes. Need to find a more elegant way to do this.