Some cleanup for

Author: denis-yuen

README.md

@@ -1,3 +1,11 @@
 ## About container-host-bag
 
 This project consists of a set of Ansible playbooks that allow you to deploy a host running Docker and the [Consonance](https://github.com/Consonance/consonance) worker daemon.  This host then is capable of running jobs scheduled out to Consonance, a cloud orchestration system capable of managing large fleets of worker hosts on clouds.  These jobs are any tools or workflows available at [Dockstore](https://dockstore.org).  See the [Consonance](https://github.com/Consonance/consonance) project page for more information.
+
+### Usage
+
+Run the ansible playbook with the following command
+
+```
+ansible-playbook -i inventory install.yml --extra-vars="@params-consonance2.json"
+```

example_params.json

@@ -72,36 +72,6 @@
     - { role: swap-enabled, when: swap_on and ansible_swaptotal_mb < 9000 }
     - { role: java, java_provider: Oracle8 }
     - { role: install-docker }
-#    - { role: seqware-container }
-#    - { role: workflow-dewrapper-dependencies, when: (workflow_name is defined and 'DEWrapper' in workflow_name ) }
-
-
-#- hosts: master:worker
-#  become: yes
-#  become_user: root
-#  vars:
-#    user_name: ubuntu
-#  tasks:
-#    - name: Copy gnos.pem keys to worker
-#      copy: src={{ item }} dest=/home/{{ user_name }}/.gnos/ owner={{ user_name }} group={{ user_name }}
-#      with_fileglob:
-#        - /home/{{ user_name }}/.gnos/*
-
-#- hosts: master
-#  become: yes
-#  become_user: root
-#  vars:
-#    installed_workflows_path: /workflows
-#    target_workflow_path: /workflows
-#    user_name: ubuntu
-#  roles:
-#    - { role: workflow, when: http_workflows is defined or s3_workflows is defined }
-
-#- hosts: master
-#  become: yes
-#  become_user: root
-#  roles:
-#    - { role: containers, when: containers is defined or http_containers is defined or s3_containers is defined }
 
 # Install monitoring components onto the client, once it is set up with all necessary containers. Maybe should happen before the consonance stuff...
 # Not strictly needed for consonance 2 development
@@ -114,7 +84,3 @@
   become_user: root
   roles:
     - { role: consonance }
-
-#- hosts: master
-#  roles:
-#    - { role: test, when: test_workflows is defined and test_workflows }

example_params_bwa.json

@@ -1,20 +1,12 @@
 {
-  "SENSU_SERVER_IP_ADDRESS": "",
   "FLEET_NAME": "broken_sword",
   "aws_key": "FOOBAR",
   "aws_secret_key": "FOOBAR",
-  "seqware_version": "1.1.1",
-  "workflow_name": "DEWrapper",
-  "workflows": [
-    "Workflow_Bundle_HelloWorld_1.0-SNAPSHOT_SeqWare_1.1.0"
-  ],
-  "install_workflow": "false",
-  "test_workflows": "false",
   "queueHost": "192.168.0.208",
   "queueName": "consonance_arch",
   "lvm_device_whitelist": "/dev/xvdb,/dev/xvdc,/dev/xvdd,/dev/xvde",
   "single_node_lvm": false,
-  "consonance_arch_version": "2.0-alpha.9",
+  "consonance_arch_version": "2.0-alpha.11",
   "seqware_engine": "whitestar",
   "seqware_use_custom_settings": false,
   "azure": false

install.yml

@@ -1,7 +1,6 @@
 ---
 - 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
-  #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
+  get_url: url=https://github.com/Consonance/consonance/releases/download/{{ 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 "".
 - name: Conditionally turn endless_worker_flag on
@@ -42,32 +41,37 @@
     - /home/ubuntu/.gnos/*
     - /home/ubuntu/.aws/*
 
+- name: Install setuptools
+  pip: name=setuptools executable=pip2.7 version=34.2.0
+
 - name: Install avro
   pip: name=avro executable=pip2.7 version=1.8.1
 
 - name: Install schema-salad
-  pip: name=schema-salad executable=pip2.7 version=1.14.20160708181155
+  pip: name=schema-salad executable=pip2.7 version=2.2.20170222151604
 
 - name: Install cwltool
-  pip: name=cwltool executable=pip2.7 version=1.0.20160712154127
+  pip: name=cwltool executable=pip2.7 version=1.0.20170217172322
+
+  # this part is fragile and did not survive the new cwltool versions (i.e. cannot resolve equivalent of merge conflict)
 
-- 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 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 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: 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 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 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
+#- name: Delete compiled main files
+#  command: rm -f /usr/local/lib/python2.7/dist-packages/cwltool/main.pyc
 
 # install dcc-storage
 

params-consonance2.json

@@ -10,8 +10,4 @@ preworkerSleep=5
 postworkerSleep=5
 max-runs=1
 hostUserName={{ hostUser }}
-endless=false
-# If you do not specify an engine, the whitestar engine will be used by default.
-seqware-engine={{ seqware_engine }}
-# Only enable seqware-settings-file if you actually have one.
-#seqware-settings-file=/home/ubuntu/.seqware/settings
+endless=false

roles/consonance/tasks/main.yml

@@ -1,10 +1,6 @@
 ---
-#consonance_arch_version: 1.1-alpha.5
-#queueName: pancancer_arch_3
-#queueHost: "{{ lookup('env','PUBLIC_IP_ADDRESS') }}"
 queueUser: queue_user
 queuePassword: queue
 hostUser: ubuntu
-seqware_engine: whitestar
 dcc_storage_version: 0.0.48
 dcc_target: collab