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SolomonShorser-OICRSolomonShorser-OICR
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Merge branch 'release/0.1.2'
2 parents 0b3424f + 26b125c commit ebb8369

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Lines changed: 119 additions & 21 deletions

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‎CHANGELOG.md‎

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# Changes
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## 0.1.2
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- New version of architecture-setup: [3.1.13](https://github.com/ICGC-TCGA-PanCancer/architecture-setup/releases/tag/3.1.13)
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- Updated config file: now includes OxoG for Collaboratory, as well as updates to other workflows' configurations.
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- Changed path to server-tags to be absolute path, in mustache file.
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## 0.1.1
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- Added the begining of an OpenStack-specific config document.
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- Fixed incorrect consonance version number in mustache file.

‎config/workflowlist.json‎

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"image":"d696eb26-a0b0-4533-a28f-60e92f9ed125",
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"instance-type":"m1.xlarge",
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"lvm_devices":""
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}
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},
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"collaboratory":
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{
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"image":"cc9c3069-3482-40b7-a0f9-80138a74a894",
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"instance-type":"c1.medium",
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"lvm_devices":""
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}
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},
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"azure":
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{
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"lvm_devices":"/dev/xvdb,/dev/xvdc"
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},
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"openstack":{
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"image":"ami-f583d190",
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"instance-type":"r3.8xlarge",
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"lvm_devices":"/dev/xvdb,/dev/xvdc"
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"sweng":
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{
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"image":"d696eb26-a0b0-4533-a28f-60e92f9ed125",
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"instance-type":"m1.2xlarge",
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"lvm_devices":""
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}
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},
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"azure":{
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"image":"ami-f583d190",
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"instance-type":"r3.8xlarge",
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"image":"sanger-base-image-2",
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"instance-type":"Standard_G5",
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"lvm_devices":"/dev/sdb"
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}
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},
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"image_name": "pancancer/seqware_whitestar_pancancer:1.1.2"
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}
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},
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"default-ini":"https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/Seqware-BWA-Workflow/feature/solomon_BWA_use_S3/workflow/config/workflow_s3.ini",
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"default-ini":"https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/Seqware-BWA-Workflow/2.6.6/workflow/config/workflow_s3.ini",
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"cloud-specific-details": {
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"aws": {
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"image":"ami-4387d526",
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"lvm_devices":"/dev/sdb"
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},
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"openstack": {
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"image":"somethingelse",
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"instance-type":"m1.xlarge",
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"lvm_devices":"/dev/xvdb,/dev/xvdc,/dev/xvdd,/dev/xvde"
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"sweng":
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{
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"image":"d696eb26-a0b0-4533-a28f-60e92f9ed125",
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"instance-type":"m1.xlarge",
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"lvm_devices":""
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}
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}
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}
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},
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"url":"s3://oicr.docker.private.images/dkfz_dockered_workflows_1.3.tar"
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}
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},
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"ami_id":"ami-d05e75b8",
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"default-ini":"https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/DEWrapperWorkflow/develop/workflow/config/DEWrapperWorkflow_1.6.0_GNOS.ini",
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"instance-type":"r3.8xlarge",
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"lvm_devices":"/dev/xvdb,/dev/xvdc"
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"cloud-specific-details": {
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"aws": {
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"image":"ami-f583d190",
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"instance-type":"r3.8xlarge",
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"lvm_devices":"/dev/xvdb,/dev/xvdc"
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},
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"azure": {
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"image":"base-image",
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"instance-type":"Standard_G5",
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"lvm_devices":"/dev/sdb"
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},
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"openstack": {
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"sweng":
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{
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"image":"d696eb26-a0b0-4533-a28f-60e92f9ed125",
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"instance-type":"m1.4xlarge",
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"lvm_devices":""
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}
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}
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},
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"default-ini":"https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/DEWrapperWorkflow/develop/workflow/config/DEWrapperWorkflow_1.6.0_GNOS.ini"
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},
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"Broad_1.0.0":
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{
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"default-ini":"https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/BroadWrapperWorkflow/develop/workflow/config/BroadWrapperWorkflow.ini",
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"instance-type":"m1.xlarge",
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"lvm_devices":"/dev/xvdb,/dev/xvdc,/dev/xvdd,/dev/xvde"
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}
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}
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},
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"OxoG_1.0":
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{
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"full_name":"Workflow_Bundle_OxoGWrapper_1.0_SeqWare_1.1.2",
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"cloud-specific-details":
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{
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"aws":
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{
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"image":"ami-b180b1db",
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"instance-type":"m2.4xlarge",
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"lvm_devices":"/dev/xvdb,/dev/xvdc"
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},
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"openstack":
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{
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"collaboratory":
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{
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"image":"a3749ea3-46c3-4d20-9b32-70ed6d584e9c",
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"instance-type":"c1.large",
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"lvm_devices":""
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}
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}
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},
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"containers":
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{
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"compbio_ngseasy_base":
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{
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"name":"compbio_ngseasy_base",
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"image_name":"compbio/ngseasy-base:a1.0-002"
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},
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"icgc_storage_client":
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{
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"name":"icgc_storage_client",
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"image_name":"icgc/icgc-storage-client"
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},
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"seqware_whitestar_pancancer":
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{
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"name":"seqware_whitestar_pancancer",
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"image_name":"pancancer/seqware_whitestar_pancancer:1.1.2-actual-java8"
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},
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"annotator":
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{
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"name":"annotator",
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"image_name":"ljdursi/pcawg-annotate"
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},
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"pancancer_upload_download":
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{
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"name":"pancancer_upload_download",
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"image_name":"pancancer/pancancer_upload_download:1.7"
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}
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},
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"http_workflow":
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{
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"url":"https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/Workflow_Bundle_OxoGWrapper_1.0.0_SeqWare_1.1.2.zip",
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"version":"1.0.0"
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},
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"default-ini":"https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/OxoGWrapperWorkflow/develop/workflow/config/OxoGWrapperWorkflow.ini"
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}
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}

‎scripts/commands/generator.py‎

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import workflowlister
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import json
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import os
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import sys
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class Generator(cliff.command.Command):
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"This Generator will generate new job orders based on the contents of ~/ini-dir. Be aware that it will also rewrite your params.json file and your ~.youxia/config file."
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cloud_specific_details = workflow_details['cloud-specific-details']['aws']
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elif cloud_env == 'OPENSTACK' :
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# If there is only one OpenStack choice, we'll just go with that.
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if len(workflow_details['cloud-specific-details']['openstack'].keys())<=1:
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cloud_specific_details = workflow_details['cloud-specific-details']['openstack'][0]
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self.log.debug('OpenStack options: '+str(workflow_details['cloud-specific-details']['openstack']))
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if len(workflow_details['cloud-specific-details']['openstack'].keys())==0:
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print('No OpenStack environments are available. Exiting.')
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sys.exit(1)
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elif len(workflow_details['cloud-specific-details']['openstack'].keys())==1:
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k = list(workflow_details['cloud-specific-details']['openstack'].keys())[0]
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cloud_specific_details = workflow_details['cloud-specific-details']['openstack'][k]
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else:
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# Check to see if the user did not provide an OpenStack environment name, or if it's not in the list of *actual* names
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if os_env_name is None or os_env_name not in workflow_details['cloud-specific-details']['openstack']:

‎scripts/install_bootstrap‎

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#! /bin/bash
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set -e
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PANCANCER_LAUNCHER_VERSION=3.2.1
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PANCANCER_CLI_VERSION=0.1.1
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PANCANCER_LAUNCHER_VERSION=3.2.2
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PANCANCER_CLI_VERSION=0.1.2
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WORKFLOW_LISTING_URL=https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/cli/${PANCANCER_CLI_VERSION}/config/workflowlist.json
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cat <<MSG

‎scripts/pancancer_config.mustache‎

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"provision":
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{
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"max_running_containers":{{max_fleet_size}},
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"youxia_deployer_parameters":"--max-spot-price {{spot_price}}{{^spot_price}}0.001{{/spot_price}} --batch-size 3 --ansible-playbook /home/ubuntu/architecture-setup/container-host-bag/install.yml -e /home/ubuntu/params.json --server-tag-file server-tags.json {{youxia_env_opt}}",
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"youxia_deployer_parameters":"--max-spot-price {{spot_price}}{{^spot_price}}0.001{{/spot_price}} --batch-size 3 --ansible-playbook /home/ubuntu/architecture-setup/container-host-bag/install.yml -e /home/ubuntu/params.json --server-tag-file /home/ubuntu/arch3/server-tags.json {{youxia_env_opt}}",
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"youxia_reaper_parameters":"{{youxia_env_opt}}",
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"reap_failed_workers":""
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}

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