--- AWSTemplateFormatVersion: 2010-09-09 Description: This is the Biotech Blueprint Informatics Service Catalog template that creates a Serivce Catalog portfolio and stocks it with a variety of informatics components you can easily deploy. Metadata: AWS::CloudFormation::Interface: ParameterGroups: - Label: default: AWS Quick Start Configuration Parameters: - QSS3BucketName - QSS3BucketRegion - QSS3KeyPrefix ParameterLabels: QSS3BucketName: default: Quick Start S3 Bucket Name QSS3BucketRegion: default: Quick Start S3 bucket region QSS3KeyPrefix: default: Quick Start S3 Key Prefix Parameters: QSS3BucketName: AllowedPattern: ^[0-9a-zA-Z]+([0-9a-zA-Z-]*[0-9a-zA-Z])*$ ConstraintDescription: Quick Start bucket name can include numbers, lowercase letters, uppercase letters, and hyphens (-). It cannot start or end with a hyphen (-). Default: aws-quickstart Description: S3 bucket name for the Quick Start assets. Quick Start bucket name can include numbers, lowercase letters, uppercase letters, and hyphens (-). It cannot start or end with a hyphen (-). Type: String QSS3BucketRegion: Default: 'us-east-1' Description: 'The AWS Region where the Quick Start S3 bucket (QSS3BucketName) is hosted. When using your own bucket, you must specify this value.' Type: String QSS3KeyPrefix: AllowedPattern: ^[0-9a-zA-Z-/]*$ ConstraintDescription: Quick Start key prefix can include numbers, lowercase letters, uppercase letters, hyphens (-), and a forward slash (/) at the end of the prefix. Default: quickstart-biotech-blueprint/ Description: S3 key prefix for the Quick Start assets. Quick Start key prefix can include numbers, lowercase letters, uppercase letters, hyphens (-), and forward slash (/). Type: String Conditions: UsingDefaultBucket: !Equals [!Ref QSS3BucketName, 'aws-quickstart'] Resources: PorfolioBB: Type: "AWS::ServiceCatalog::Portfolio" Properties: ProviderName: AWS Description: Collection of Bio and Chem informatics tools assembled by AWS to make life easier for biotechs. DisplayName: Biotech Blueprint Informatics Tools ChemAxonProduct: Type: "AWS::ServiceCatalog::CloudFormationProduct" Properties: Owner: ChemAxon Description: ChemAxon's Compound Registration is a system built on a set of web services, aiding users to register molecular structures into a compound database. The registration process spots unique compounds among a set of structures already contained within the database. Distributor: AWS SupportDescription: "You need to subscribe to the ChemAxon marketplace AMI before you can deploy this software. https://aws.amazon.com/marketplace/pp/B077F6VV3B?qid=1553611079631&sr=0-1&ref_=srh_res_product_title." SupportUrl: "https://chemaxon.com/support" SupportEmail: support@chemaxon.com Name: ChemAxon Compound Registry ProvisioningArtifactParameters: - Info: LoadTemplateFromURL: !Sub - 'https://${S3Bucket}.s3.${S3Region}.${AWS::URLSuffix}/${QSS3KeyPrefix}templates/bb.chemaxon-registry.template.yaml' - S3Region: !If [UsingDefaultBucket, !Ref 'AWS::Region', !Ref QSS3BucketRegion] S3Bucket: !If [UsingDefaultBucket, !Sub '${QSS3BucketName}-${AWS::Region}', !Ref QSS3BucketName] ChemAxonProductAssociation: Type: "AWS::ServiceCatalog::PortfolioProductAssociation" Properties: PortfolioId: !Ref PorfolioBB ProductId: !Ref ChemAxonProduct BenchlingProduct: Type: "AWS::ServiceCatalog::CloudFormationProduct" Properties: Owner: AWS Description: Benchling Biotech Blueprint template to automate creating PrivateLink and split horizon DNS configs to Benchling's SaaS platform. Distributor: Benchling SupportUrl: https://benchling.com/enterprise Name: Benchling ProvisioningArtifactParameters: - Info: LoadTemplateFromURL: !Sub - 'https://${S3Bucket}.s3.${S3Region}.${AWS::URLSuffix}/${QSS3KeyPrefix}templates/bb.benchling-platform.template.yaml' - S3Region: !If [UsingDefaultBucket, !Ref 'AWS::Region', !Ref QSS3BucketRegion] S3Bucket: !If [UsingDefaultBucket, !Sub '${QSS3BucketName}-${AWS::Region}', !Ref QSS3BucketName] BenchlingProductAssociation: Type: "AWS::ServiceCatalog::PortfolioProductAssociation" Properties: PortfolioId: !Ref PorfolioBB ProductId: !Ref BenchlingProduct NextflowProduct: Type: "AWS::ServiceCatalog::CloudFormationProduct" Properties: Owner: AWS Description: Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. Distributor: Comparative Bioinformatics group at the Barcelona Centre for Genomic Regulation (CRG). SupportUrl: https://github.com/aws-samples/aws-genomics-workflows Name: Nextflow ProvisioningArtifactParameters: - Info: LoadTemplateFromURL: !Sub - 'https://${S3Bucket}.s3.${S3Region}.${AWS::URLSuffix}/${QSS3KeyPrefix}submodules/quickstart-nextflow/templates/bb.nextflow.template' - S3Region: !If [UsingDefaultBucket, !Ref 'AWS::Region', !Ref QSS3BucketRegion] S3Bucket: !If [UsingDefaultBucket, !Sub '${QSS3BucketName}-${AWS::Region}', !Ref QSS3BucketName] NextflowProductAssociation: Type: "AWS::ServiceCatalog::PortfolioProductAssociation" Properties: PortfolioId: !Ref PorfolioBB ProductId: !Ref NextflowProduct TitianMosaicProduct: Type: "AWS::ServiceCatalog::CloudFormationProduct" Properties: Owner: "Titian Software Limited" Description: "Mosaic FreezerManagement is a comprehensive and cost-effective software solution for managing and tracking all types of sample inventory, backed by a full audit trail. It provides a flexible interface to define and record properties for any type of sample or container, and manages your entire hierarchy of storage including freezers, shelves, cupboards, etc. Other features include an intuitive search interface, and expiry date tracking. IMPORTANT NOTE: Please contact Titian at info@titian.co.uk for validation before you launch the template below, otherwise the template will fail." Distributor: "Titian Software Limited" SupportUrl: "https://www.titian.co.uk/resourcesandsupport/support-services" SupportDescription: "Titian supports a worldwide customer base – including customer sites in Europe, USA and Asia. Support may be provided by email, telephone or shared desktop sessions." SupportEmail: "info@titian.co.uk" Name: "Mosaic FreezerManagement" ProvisioningArtifactParameters: - Info: LoadTemplateFromURL: !Sub - 'https://${S3Bucket}.s3.${S3Region}.${AWS::URLSuffix}/${QSS3KeyPrefix}submodules/quickstart-titian-mosaic/templates/bb.titian-mosaic.template' - S3Region: !If [UsingDefaultBucket, !Ref 'AWS::Region', !Ref QSS3BucketRegion] S3Bucket: !If [UsingDefaultBucket, !Sub '${QSS3BucketName}-${AWS::Region}', !Ref QSS3BucketName] TitianProductAssociation: Type: "AWS::ServiceCatalog::PortfolioProductAssociation" Properties: PortfolioId: !Ref PorfolioBB ProductId: !Ref TitianMosaicProduct DotmaticsProduct: Type: "AWS::ServiceCatalog::CloudFormationProduct" Properties: Owner: "Dotmatics" Description: "Dotmatics Suite running on AWS. Please contact sales@dotmatics.com for licensing details." Distributor: "Dotmatics" SupportUrl: "https://support.dotmatics.com" SupportDescription: "Support is provided through our usual channels – please visit our support pages or drop us an email." SupportEmail: "support@dotmatics.com" Name: "Dotmatics Suite" ProvisioningArtifactParameters: - Info: LoadTemplateFromURL: !Sub - 'https://${S3Bucket}.s3.${S3Region}.${AWS::URLSuffix}/${QSS3KeyPrefix}submodules/quickstart-dotmatics/templates/bb.dotmatics.template' - S3Region: !If [UsingDefaultBucket, !Ref 'AWS::Region', !Ref QSS3BucketRegion] S3Bucket: !If [UsingDefaultBucket, !Sub '${QSS3BucketName}-${AWS::Region}', !Ref QSS3BucketName] DotmaticsProductAssociation: Type: "AWS::ServiceCatalog::PortfolioProductAssociation" Properties: PortfolioId: !Ref PorfolioBB ProductId: !Ref DotmaticsProduct