Merge pull request #63 from Integrative-Transcriptomics:adapting-wiggle-visualization

Adapting-wiggle-visualization

Author: mwittep

.github/workflows/docker.yml

@@ -3,7 +3,7 @@ name: Build and Push Docker Image
 # when to run the workflow
 on:
   push:
-    branches: [main]
+    branches: [main_2]
 
 # the jobs to run
 jobs:

.github/workflows/docker_release.yml

@@ -0,0 +1,48 @@
+name: Build and Push Docker Image
+
+# when to run the workflow
+on:
+  push:
+    branches: [main]
+
+# the jobs to run
+jobs:
+  build:
+    # the os to run the job on
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      # build the image now
+      - name: Build Docker image
+        env:
+          YARNRC: ${{secrets.YARNRC}}
+        run: |
+          echo "$YARNRC" > .yarnrc.yml
+          docker compose --env-file variables_tsspredator.env build
+
+      - name: save images
+        run: |
+          docker save tsspredator_web:latest | gzip > image_tsspredator_web.tar.gz
+          docker save tsspredator_celery_app:latest | gzip > image_tsspredator_celery_app.tar.gz
+
+      - name: Release WebImage to Repo
+        uses: svenstaro/upload-release-action@v2
+        with:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          file: image_tsspredator_web.tar.gz
+          asset_name: TSSpredatorWeb
+          tag: ${{ github.ref }}
+          overwrite: true
+          body: "The image for the web interface of TSSpredator"
+
+      - name: Release CeleryImage to Repo
+        uses: svenstaro/upload-release-action@v2
+        with:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          file: image_tsspredator_celery_app.tar.gz
+          asset_name: TSSpredatorCelery
+          tag: ${{ github.ref }}
+          overwrite: true
+          body: "The image for the celery app of TSSpredator"

.gitignore

@@ -2,16 +2,19 @@
 
 # dependencies
 node_modules
+.yarn
 /.pnp
 .pnp.js
 env
+/.vite
 
 # testing
 /coverage
 
 # production
 /build
 /data
+/dist
 
 # misc
 .DS_Store
@@ -24,12 +27,19 @@ __pycache__
 npm-debug.log*
 yarn-debug.log*
 yarn-error.log*
-server_tsspredator/exampleData/campylobacter/Archive/*
-server_tsspredator/exampleData/pseudomonas/Archive/*
+server_tsspredator/exampleData/campylobacter/files/*
+server_tsspredator/exampleData/pseudomonas/files/*
 dump.rdb
 package-lock.json
 server_tsspredator.egg-info/PKG-INFO
 celerybeat-schedule.db
 server_tsspredator/exampleData/campylobacter/files.zip
 server_tsspredator/exampleData/pseudomonas/files.zip
 server_tsspredator.egg-info
+.npmrc
+.gradle
+bin
+.yarnrc.yml
+image_tsspredator_celery_app.tar.gz
+image_tsspredator_web.tar.gz
+server_tsspredator/redisdb/dump-tsspredator.rdb

.vite/deps_temp_b8ec2e2a/package.json

@@ -0,0 +1,3 @@
+{
+  "type": "module"
+}

celery/dockerfile

@@ -1,7 +1,7 @@
 
 # first stage build the frontend
 # FROM node:20-alpine3.18 as build
-FROM --platform=linux/amd64 alpine:3.18
+FROM --platform=linux/x86_64 alpine:latest
 
 # Set the working directory in the container to /app
 # Set the working directory in the container to /app
@@ -27,17 +27,21 @@ COPY server_tsspredator /app/server_tsspredator
 COPY requirements.txt /app
 COPY setup.py /app
 COPY server_tsspredator/TSSpredator.jar /app
-
+RUN apk add gcompat libbz2 libcurl libstdc++ krb5-dev zlib gcc musl-dev g++ curl-dev
+RUN wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig -P /app
+RUN chmod +x /app/bedGraphToBigWig
 
 # Install java 17
 RUN apk add --update --no-cache openjdk17-jre-headless
 
 
 # Install python3.11
-RUN apk add --update --no-cache python3 py3-pip
-
+RUN apk add --update --no-cache python3-dev py3-pip
+RUN python3 -m venv /app/env_tss_predator_celery
+ENV PATH="/app/env_tss_predator_celery/bin:$PATH"
+RUN python3 -m pip install --upgrade pip
 # install python dependencies
-RUN pip install -r requirements.txt
+RUN python3 -m pip install -r requirements.txt
 
 # Install the server package
 RUN pip install -e .

docker-compose.yml

@@ -2,11 +2,12 @@ version: '3.8'
 services:
   web:
     image: tsspredator_web:latest
+    platform: linux/x86_64
     build:
       context: .
       dockerfile: webapp/Dockerfile
     working_dir: /app/server_tsspredator
-    command: gunicorn --workers 6 --timeout 500 --graceful-timeout 500   --bind 0.0.0.0:5001 server_tsspredator.wsgi:tsspredator
+    command: gunicorn --workers 6 --timeout 500 --graceful-timeout 500  --bind 0.0.0.0:5001 server_tsspredator.wsgi:tsspredator
     deploy:
       resources:
         limits:
@@ -33,6 +34,7 @@ services:
 
   celery:
     image: tsspredator_celery_app:latest
+    platform: linux/x86_64
     build:
       context: .
       dockerfile: celery/Dockerfile

public/index.html renamed to index.html

@@ -4,22 +4,21 @@
 <head>
   <link rel="stylesheet" href="https://esm.sh/higlass@1.13/dist/hglib.css" />
   <meta charset="utf-8" />
-  <link rel="icon" href="%PUBLIC_URL%/favicon.ico" />
+  <link rel="icon" href="/favicon.ico" />
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="theme-color" content="#000000" />
-  <meta name="description" content="Web site created using create-react-app" />
-  <link rel="apple-touch-icon" href="%PUBLIC_URL%/logo192.png" />
+  <link rel="apple-touch-icon" href="/logo192.png" />
   <!--
       manifest.json provides metadata used when your web app is installed on a
       user's mobile device or desktop. See https://developers.google.com/web/fundamentals/web-app-manifest/
     -->
-  <link rel="manifest" href="%PUBLIC_URL%/manifest.json" />
+  <link rel="manifest" href="/manifest.json" />
   <!--
-      Notice the use of %PUBLIC_URL% in the tags above.
+      Notice the use of  in the tags above.
       It will be replaced with the URL of the `public` folder during the build.
       Only files inside the `public` folder can be referenced from the HTML.
 
-      Unlike "/favicon.ico" or "favicon.ico", "%PUBLIC_URL%/favicon.ico" will
+      Unlike "/favicon.ico" or "favicon.ico", "/favicon.ico" will
       work correctly both with client-side routing and a non-root public URL.
       Learn how to configure a non-root public URL by running `npm run build`.
     -->
@@ -39,6 +38,7 @@
       To begin the development, run `npm start` or `yarn start`.
       To create a production bundle, use `npm run build` or `yarn build`.
     -->
+	<script type="module" src="/src/index.jsx"></script>
 </body>
 
 </html>