Merge pull request #112 from rasools/OMICSINT_H24

Add session_ml_deep_learning_integration_amd workflow

Author: rasools

.github/workflows/docker-build-lab-Single_cell-amd.yml

@@ -0,0 +1,63 @@
+name: Build and Push Docker Image for lab single cell 
+
+on:
+  push:
+    paths:
+      - 'session_ml/SingleCell/**'
+    branches:
+      - OMICSINT_H24
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    if: github.repository == 'NBISweden/workshop_omics_integration'
+
+    steps:
+      # Checkout the repository
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Set up Docker Buildx for multi-platform builds
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      # Log in to Docker Hub using the secrets
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }} 
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      # Log in to GitHub Container Registry (GHCR)
+      - name: Log in to GHCR
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Build and push the Docker image for both amd64 to Docker Hub
+      - name: Build and Push Docker Image to Docker Hub
+        uses: docker/build-push-action@v4
+        with:
+          context: ./session_ml/SingleCell
+          file: session_ml/SingleCell/Dockerfile
+          platforms: linux/amd64
+          push: true
+          no-cache: true
+          tags: docker.io/rasoolsnbis/omicsint_h24:session_ml_single_cell_amd
+
+      # Build and push the Docker image to GitHub Container Registry (GHCR)
+      - name: Build and Push Docker Image to GHCR
+        uses: docker/build-push-action@v4
+        with:
+          context: ./session_ml/SingleCell
+          file: session_ml/SingleCell/Dockerfile
+          platforms: linux/amd64
+          push: true
+          no-cache: true
+          tags: ghcr.io/${{ github.repository_owner }}/omicsint_h24:session_ml_single_cell_amd
+
+      - name: Inspect Docker Image
+        run: docker buildx imagetools inspect docker.io/rasoolsnbis/omicsint_h24:session_ml_single_cell_amd

session_ml/SingleCell/Dockerfile

@@ -15,6 +15,7 @@ RUN export DEBIAN_FRONTEND=noninteractive \
     && apt-get -yq update \
     && apt-get -yq install --no-install-recommends \
       curl \
+      wget \
       dpkg-sig \
       libpq5 \
       psmisc \
@@ -69,6 +70,13 @@ RUN mamba env create -f /tmp/SingleCell_env.yml && rm /tmp/SingleCell_env.yml
 RUN R -e "install.packages('remotes', repos='http://cran.us.r-project.org')"
 RUN R -e "remotes::install_github('satijalab/seurat-data')"
 
+# Download required files to the data directory
+RUN mkdir -p /home/jovyan/lab/data \
+    && wget -O /home/jovyan/lab/data/google_drive_file.csv "https://drive.google.com/uc?export=download&id=1hBeh2L5PC-T87YObCmJv4Qcm59IqkkOf" \
+    && wget -O /home/jovyan/lab/data/atac_v1_pbmc_10k_singlecell.csv "https://cf.10xgenomics.com/samples/cell-atac/1.0.1/atac_v1_pbmc_10k/atac_v1_pbmc_10k_singlecell.csv" \
+    && wget -O /home/jovyan/lab/data/atac_v1_pbmc_10k_filtered_peak_bc_matrix.h5 "https://cf.10xgenomics.com/samples/cell-atac/1.0.1/atac_v1_pbmc_10k/atac_v1_pbmc_10k_filtered_peak_bc_matrix.h5" \
+    && wget -O /home/jovyan/lab/data/pbmc_10k_v3.rds "https://www.dropbox.com/s/3f3p5nxrn5b3y4y/pbmc_10k_v3.rds?dl=1"
+
 # Download and install RStudio Server
 RUN curl -sL "https://download2.rstudio.org/server/focal/${RSTUDIO_ARCH}/rstudio-server-${RSTUDIO_VERSION//+/-}-${RSTUDIO_ARCH}.deb" -o /tmp/rstudio-server.deb && \
     echo "64044984a5791690586e21bf4411019ed3dccaf32a69e0838090762f3eba8da0  /tmp/rstudio-server.deb" | sha256sum -c - && \
@@ -113,4 +121,4 @@ RUN chown -R ${USER}:${GROUP} ${HOME}/lab \
 USER ${USER}
 EXPOSE 8787
 
-ENTRYPOINT ["/etc/run.sh"]
+ENTRYPOINT ["/etc/run.sh"]

session_ml/SingleCell/lab/SingleCell_OmicsIntegration.Rmd

@@ -48,18 +48,7 @@ library("Seurat")
 library("ggplot2")
 library("Signac")
 
-
-#### Data download #################################################################################
-# You need to download the following file and include it in the same directory as this notebook
-#
-# https://drive.google.com/uc?export=download&id=1hBeh2L5PC-T87YObCmJv4Qcm59IqkkOf
-#
-####################################################################################################
-
-#After downloading the file above, download the following:
-#download.file('https://cf.10xgenomics.com/samples/cell-atac/1.0.1/atac_v1_pbmc_10k/atac_v1_pbmc_10k_singlecell.csv', method = 'wget', destfile = 'atac_v1_pbmc_10k_singlecell.csv')
-#download.file('https://cf.10xgenomics.com/samples/cell-atac/1.0.1/atac_v1_pbmc_10k/atac_v1_pbmc_10k_filtered_peak_bc_matrix.h5', method = 'wget', destfile = 'atac_v1_pbmc_10k_filtered_peak_bc_matrix.h5')
-#download.file('https://www.dropbox.com/s/3f3p5nxrn5b3y4y/pbmc_10k_v3.rds?dl=1', method = 'wget', destfile = 'pbmc_10k_v3.rds')
+####################################################################################
 
 #Gene activity quantification (ATACseq peaks)
 peaks <- Read10X_h5("data/atac_v1_pbmc_10k_filtered_peak_bc_matrix.h5")