diff --git a/.gitignore b/.gitignore index 7a71ed3..ab8be6a 100644 --- a/.gitignore +++ b/.gitignore @@ -5,5 +5,4 @@ **.bkp shinyproxy/shiny-apps -shinyproxy/application.yml nginx/nginx.conf diff --git a/shinyproxy/.gitignore b/shinyproxy/.gitignore index e699518..d392f0e 100644 --- a/shinyproxy/.gitignore +++ b/shinyproxy/.gitignore @@ -1,2 +1 @@ *.jar -application.yml diff --git a/shinyproxy/application.yml b/shinyproxy/application.yml new file mode 100644 index 0000000..a080d0b --- /dev/null +++ b/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 + diff --git a/shinyproxy/templates/index.html b/shinyproxy/templates/index.html index 465d34f..c7e399f 100644 --- a/shinyproxy/templates/index.html +++ b/shinyproxy/templates/index.html @@ -137,7 +137,7 @@

Impact (examples): - Neurobiology + Neurobiology Splicing Regulation Cancer @@ -202,7 +202,7 @@

Impact (examples):
- Cancer + Cancer

@@ -220,7 +220,9 @@

- Tutorial + Paper + GitHub + Tutorial

@@ -233,7 +235,6 @@

-
@@ -248,7 +249,12 @@

- Tutorial + Paper + GitHub + + Tutorial + [1] + [2]

@@ -265,8 +271,8 @@

Impact (examples):
Alternative Splicing - [1] - [2] + [1] + [2]

@@ -306,10 +312,30 @@

- +
+
+

+ + + + markeR +

+ + +

+ GitHub +

+ + +

Toolkit for Evaluating Gene Signatures as Phenotype Markers in R

+
+
+ +
-
--> +