Update application.yml and index.html (#36)

* update gitignore to not ignore application.yml

* update index.html with new apps

* update application.yml

Author: ritamtbsilva

shinyproxy/.gitignore

@@ -1,2 +1 @@
 *.jar
-application.yml

shinyproxy/application.yml

@@ -0,0 +1,156 @@
+# more info at https://shinyproxy.io/documentation/configuration
+
+spring.application.name: NMorais Lab - Bioinformatic Apps
+spring:
+  servlet:
+    multipart:
+      max-file-size: 200MB
+      max-request-size: 200MB
+
+proxy: 
+  title: NMorais Lab - Bioinformatic Apps
+  port: 8080
+  # bind-address: 127.0.0.1
+  hide-navbar: false
+  template-path: /opt/shinyproxy/templates
+  container-wait-time: 30000
+  container-log-path: /container-logs
+  usage-stats-url: micrometer
+
+  # app recovery enabled
+  stop-proxies-on-shutdown: false
+  recover-running-proxies: true
+
+  docker:
+    internal-networking: true
+    container-network: shiny-net
+  specs:
+  - id: psichomics
+    description: Alternative splicing quantification, visualisation and analysis
+    container-image: nunoagostinho/psichomics:1.28.1
+    container-cmd: ["R", "-e", "psichomics::psichomics(host='0.0.0.0', port=3838, shinyproxy=TRUE, cache='~/Downloads/AnnotationHub')"]
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/psichomics/data:/root/Downloads" ]
+    template-properties:
+      startup-time: 20s
+      listed: true
+  - id: voyAGEr
+    description: Analysis of age-related gene expression changes in human
+    container-image: diseasetranscriptomicslab/voyager:v2.0.2
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/voyAGEr/data:/home/app/data" ]
+    template-properties:
+      listed: true
+  - id: cTRAP
+    description: Identifying candidate causal perturbations from differential gene expression data
+    container-image: nunoagostinho/ctrap:1.14.1
+    container-network: "${proxy.docker.container-network}"
+    container-cmd: ["R", "-e", "cTRAP::cTRAP(host='0.0.0.0', port=3838, expire=30, flowerURL='http://flower:5555/flower')"]
+    container-volumes: [ "/srv/apps/cTRAP/sessions:/data" ]
+    template-properties:
+      startup-time: 15s
+      listed: true
+  - id: scStudio_MCT
+    container-image: genomeptimm/scstudio_mct:1.6
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio_MCT/datasets:/home/app/datasets" ]
+    template-properties:
+      listed: true
+  - id: scStudio
+    container-image: martabica/scstudio-home:1.2
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_DATA
+    container-image: martabica/scstudio-selectdata:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_QC
+    container-image: martabica/scstudio-qc:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_NORM
+    container-image: martabica/scstudio-normalization:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_DIMRED
+    container-image: martabica/scstudio-dimred:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_CLUSTER
+    container-image: martabica/scstudio-clustering:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_DEA
+    container-image: martabica/scstudio-dea:1.5
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_GSEA
+    container-image: martabica/scstudio-fea:1.3
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_FEATPLOT
+    container-image: martabica/scstudio-featureplots:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_SETTINGS
+    container-image: martabica/scstudio-settings:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_REPORT
+    container-image: martabica/scstudio-report:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true      
+  - id: splicingSenescenceDashboard
+    display-name: Splicing in senescence
+    description: Splicing in senescence (dashboard)
+    container-image: marianaferreira/splicing-senescence-dasboard
+    container-network: "${proxy.docker.container-network}"
+    template-properties:
+      startup-time: 20s
+      listed: false
+  - id: betAS
+    description: Intuitive differential alternative splicing analysis
+    container-image: marianaferreira/betas:v1.2.1
+    container-cmd: ["R", "-e", "betAS::betASapp(host='0.0.0.0', port=3838)"]
+    container-network: "${proxy.docker.container-network}"
+    template-properties:
+      startup-time: 5s
+      listed: true
+
+logging:
+  file:
+    name: /log/shinyproxy.log
+
+management:
+  metrics:
+    export:
+      prometheus:
+        enabled: true
+
+server:
+  secure-cookies: true
+  forward-headers-strategy: native
+  frame-options: sameorigin
+