diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 117b0812b0736e7fb7a6c1ca40524bc7dcaa1528..3925a4c5125f9f2c8ac0b1f2d1be23a96148872b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,6 +6,8 @@ services:
build:
+ except:
+ - main
stage: build
needs: []
before_script:
@@ -29,6 +31,8 @@ build:
.deploy:
+ except:
+ - main
stage: deploy
needs:
- "build"
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index 8c4d0abfe8e91a7ebaae830ec50ea42ac958c6b7..0000000000000000000000000000000000000000
--- a/Dockerfile
+++ /dev/null
@@ -1,22 +0,0 @@
-# FROM registry-gitlab.pasteur.fr/hub/rshiny-k8s:4.2.3--1.5.21.1006
-# FROM registry-gitlab.pasteur.fr/hub/rshiny-k8s:1.5.21.1006
-# FROM registry-gitlab.pasteur.fr/hub/rshiny-k8s:4.2.3
-FROM registry-gitlab.pasteur.fr/hub/rshiny-k8s:latest
-
-# install additional dependencies, comment the block if you don't have one
-RUN apt-get update \
- && apt-get install -y \
- wget \
- && rm -rf /var/lib/apt/lists/*
-
-# Copy your dependencies, destination filename must be "packages_to_install.csv"
-COPY ./my_packages_to_install.csv /opt/scripts/packages_to_install.csv
-
-# Install R packages
-RUN Rscript /opt/scripts/install_r_packages.R
-
-# grant shiny to created bookmark state directory in this directory
-RUN chown shiny:shiny /var/lib/shiny-server
-
-# Copy you shiny app
-COPY ./example_proj /srv/shiny-server
diff --git a/example_proj/app.R b/example_proj/app.R
deleted file mode 100644
index f2adac6463d32fef4666b19497a4a686fddd9a01..0000000000000000000000000000000000000000
--- a/example_proj/app.R
+++ /dev/null
@@ -1,83 +0,0 @@
-# Name : app.R
-# Folder : ~/rshiny-k8s/example_proj
-# Date : 05/04/23
-# Aim : Simple example of app developped in RShiny.
-# Authors : From Shiny Examples - Modify by Elodie C. et Bryan B.
-
-# Load packages -------------------------------------------------------------------
-library(shiny)
-library(shinythemes)
-library(ggplot2)
-
-### Try to fix error "unable to open connection to X11"
-options(bitmapType='cairo')
-
-# Show installed and loaded packages
-sessionInfo()
-
-# UI part -------------------------------------------------------------------------
-# Define UI for app that draws a histogram ----
-ui <- fluidPage(
-
- # App title ----
- titlePanel("Hello Shiny in docker image!"),
-
- # Sidebar layout with input and output definitions ----
- sidebarLayout(
-
- # Sidebar panel for inputs ----
- sidebarPanel(
-
- # Input: Slider for the number of bins ----
- sliderInput(inputId = "bins",
- label = "Number of bins:",
- min = 1,
- max = 50,
- value = 30)
-
- ),
-
- # Main panel for displaying outputs ----
- mainPanel(
-
- # Output: Histogram ----
- plotOutput(outputId = "distPlot"),
- # Output: SessionInfo fecth from server
- htmlOutput("mySessionInfo")
-
- )
- )
-)
-# Server part -------------------------------------------------------------------------
-# Define server logic required to draw a histogram ----
-server <- function(input, output) {
-
- # Histogram of the Old Faithful Geyser Data ----
- # with requested number of bins
- # This expression that generates a histogram is wrapped in a call
- # to renderPlot to indicate that:
- #
- # 1. It is "reactive" and therefore should be automatically
- # re-executed when inputs (input$bins) change
- # 2. Its output type is a plot
- output$distPlot <- renderPlot({
-
- x <- faithful$waiting
- bins <- seq(min(x), max(x), length.out = input$bins + 1)
-
- hist(x, breaks = bins, col = "#75AADB", border = "white",
- xlab = "Waiting time to next eruption (in mins)",
- main = "Histogram of waiting times")
-
- })
- output$mySessionInfo <- renderPrint({
-
- capture.output(sessionInfo())
- capture.output(capabilities())
-
- })
-
-}
-
-# Run Shiny app ----------------------------------------------------------------------
-shinyApp(ui = ui, server = server)
diff --git a/k8s/deployment.yaml b/k8s/deployment.yaml
deleted file mode 100644
index 84602730dcc34e4c706fe660f731f1baeb0250f2..0000000000000000000000000000000000000000
--- a/k8s/deployment.yaml
+++ /dev/null
@@ -1,41 +0,0 @@
----
-apiVersion: apps/v1
-kind: Deployment
-metadata:
- name: rshiny-deployment
- labels:
- app: rshiny-app
-spec:
- selector:
- matchLabels:
- app: rshiny-app
- strategy:
- type: RollingUpdate
- rollingUpdate:
- maxSurge: 1
- maxUnavailable: 0
- template:
- metadata:
- labels:
- app: rshiny-app
- spec:
- containers:
- - name: rshiny-pod
- image: registry-gitlab.pasteur.fr/hub/rshiny-k8s-example/main/example:latest
- securityContext:
- runAsGroup: 999
- runAsUser: 999
- ports:
- - name: http
- containerPort: 3838
- protocol: TCP
- resources:
- requests:
- memory: "256Mi"
- cpu: "500m"
- limits:
- memory: "512Mi"
- cpu: "500m"
- imagePullSecrets:
- - name: registry-gitlab
----
\ No newline at end of file
diff --git a/k8s/hpa.yaml b/k8s/hpa.yaml
deleted file mode 100644
index 543bf3b6edfc31eee60d91e502fc998340b2fe70..0000000000000000000000000000000000000000
--- a/k8s/hpa.yaml
+++ /dev/null
@@ -1,22 +0,0 @@
-apiVersion: autoscaling/v2beta1
-kind: HorizontalPodAutoscaler
-metadata:
- name: rkubshiny-hpa
- labels:
- app: rshiny-hpa
-spec:
- scaleTargetRef:
- apiVersion: apps/v1
- kind: Deployment
- name: rshiny-deployment
- minReplicas: 1
- maxReplicas: 4
- metrics:
- - type: Resource
- resource:
- name: cpu
- targetAverageUtilization: 80
- - type: Resource
- resource:
- name: memory
- targetAverageUtilization: 80
\ No newline at end of file
diff --git a/k8s/ingress.yaml b/k8s/ingress.yaml
deleted file mode 100644
index ba547d16bbf794f5db0c81774fc223e2f75dddd2..0000000000000000000000000000000000000000
--- a/k8s/ingress.yaml
+++ /dev/null
@@ -1,22 +0,0 @@
----
-apiVersion: networking.k8s.io/v1
-kind: Ingress
-metadata:
- annotations:
- nginx.ingress.kubernetes.io/affinity: cookie
- nginx.ingress.kubernetes.io/proxy-body-size: 256m
- name: rshiny-ingress
-spec:
- ingressClassName: internal
- rules:
- - host: rshiny-example.dev.pasteur.cloud
- http:
- paths:
- - path: /
- pathType: Prefix
- backend:
- service:
- name: rshiny-srv
- port:
- number: 8080
----
\ No newline at end of file
diff --git a/k8s/service.yaml b/k8s/service.yaml
deleted file mode 100644
index 5cf03d95444c1eb0f51eb913c468e3c2db2365bc..0000000000000000000000000000000000000000
--- a/k8s/service.yaml
+++ /dev/null
@@ -1,14 +0,0 @@
----
-apiVersion: v1
-kind: Service
-metadata:
- name: rshiny-srv
-spec:
- type: ClusterIP
- ports:
- - name: http
- port: 8080
- targetPort: 3838
- selector:
- app: rshiny-app
----
\ No newline at end of file
diff --git a/my_packages_to_install.csv b/my_packages_to_install.csv
deleted file mode 100644
index de7515ba99afba7e16aaed43bf5621e0e2fc0e00..0000000000000000000000000000000000000000
--- a/my_packages_to_install.csv
+++ /dev/null
@@ -1,5 +0,0 @@
-Package_name;Comments
-shinythemes;cran package
-ggplot2;cran package
-limma;bioconductor package
-tidyverse/tibble; github package
\ No newline at end of file