From bb4c400713780f5b934fd09bee70cf7399786f98 Mon Sep 17 00:00:00 2001
From: Geert van Geest <geert.vangeest@sib.swiss>
Date: Wed, 7 Apr 2021 13:45:48 +0200
Subject: [PATCH] added docker workflow

---
 .github/workflows/push_jupyter_container.yml | 20 ++++++++++++++++++++
 .github/workflows/push_rstudio_container.yml | 20 ++++++++++++++++++++
 Docker/jupyter/Dockerfile                    | 19 +++++++++----------
 Docker/rstudio/Dockerfile                    |  5 ++++-
 4 files changed, 53 insertions(+), 11 deletions(-)
 create mode 100644 .github/workflows/push_jupyter_container.yml
 create mode 100644 .github/workflows/push_rstudio_container.yml

diff --git a/.github/workflows/push_jupyter_container.yml b/.github/workflows/push_jupyter_container.yml
new file mode 100644
index 0000000..c15ff21
--- /dev/null
+++ b/.github/workflows/push_jupyter_container.yml
@@ -0,0 +1,20 @@
+name: Publish Docker image
+on:
+  release:
+    types: [published]
+jobs:
+  push_to_registry:
+    name: Push Docker image to GitHub Packages
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v2
+      - name: Push to GitHub Packages
+        uses: docker/build-push-action@v1
+        with:
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+          registry: docker.pkg.github.com
+          path: Docker/jupyter
+          repository: sib-swiss/ngs-longreads-training/ngs-longreads-jupyter
+          tag_with_ref: true
diff --git a/.github/workflows/push_rstudio_container.yml b/.github/workflows/push_rstudio_container.yml
new file mode 100644
index 0000000..54afc15
--- /dev/null
+++ b/.github/workflows/push_rstudio_container.yml
@@ -0,0 +1,20 @@
+name: Publish Docker image
+on:
+  release:
+    types: [published]
+jobs:
+  push_to_registry:
+    name: Push Docker image to GitHub Packages
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v2
+      - name: Push to GitHub Packages
+        uses: docker/build-push-action@v1
+        with:
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+          registry: docker.pkg.github.com
+          path: Docker/rstudio
+          repository: sib-swiss/ngs-longreads-training/ngs-longreads-rstudio
+          tag_with_ref: true
diff --git a/Docker/jupyter/Dockerfile b/Docker/jupyter/Dockerfile
index 51db5eb..9d8aa3f 100644
--- a/Docker/jupyter/Dockerfile
+++ b/Docker/jupyter/Dockerfile
@@ -1,4 +1,4 @@
-FROM jupyter/minimal-notebook
+FROM jupyter/minimal-notebook:9fe5186aba96
 
 USER root
 RUN cat /etc/skel/.bashrc >> /etc/bash.bashrc
@@ -7,24 +7,23 @@ USER $NB_UID
 RUN rm -r /home/jovyan/work
 
 RUN /opt/conda/bin/conda install -y --quiet -c bioconda \
-samtools \
-minimap2 \
-fastqc \
-pbmm2 \
-parallel
+samtools=1.10 \
+minimap2=2.17 \
+fastqc=0.11.9 \
+pbmm2=1.4.0 \
+parallel=20170422
 
 RUN parallel --citation <<< 'will cite'
 
+# install nanoplot with pip (with conda gives errors)
 RUN pip install NanoPlot
 
+# install flair environment from .yml file
 COPY flair_env.yml ./
-
 RUN /opt/conda/bin/conda env create -f flair_env.yml
-
 RUN rm flair_env.yml
 
+# install pacbio environment from .yml file
 COPY pacbio_env.yml ./
-
 RUN /opt/conda/bin/conda env create -f pacbio_env.yml
-
 RUN rm pacbio_env.yml
diff --git a/Docker/rstudio/Dockerfile b/Docker/rstudio/Dockerfile
index 7246eea..a588638 100644
--- a/Docker/rstudio/Dockerfile
+++ b/Docker/rstudio/Dockerfile
@@ -1,12 +1,15 @@
-FROM rocker/rstudio
+FROM rocker/rstudio:4.0.3
 
+# non interactive for installing dependencies
 ENV DEBIAN_FRONTEND=noninteractive
 
+# installing dependencies for DESeq2 and rmarkdown
 RUN apt-get update
 RUN apt-get install -y libz-dev
 RUN apt-get install -y libxml2-dev
 RUN apt-get install -y libxt-dev
 
+# copy and run script to install packages
 COPY install_packages.R ./
 
 RUN Rscript ./install_packages.R