From 54ba7a1f8d78dc2864f5ebadbaaf3b6c8afa58be Mon Sep 17 00:00:00 2001
From: Adam Dinan <adam1989ie@gmail.com>
Date: Wed, 12 Jun 2024 20:03:37 +0100
Subject: [PATCH 1/2] Push to Dockerhub before running test pipeline

---
 .github/workflows/ci.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 07462c7..c96f112 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -40,10 +40,6 @@ jobs:
           chmod +x nextflow
           sudo mv nextflow /usr/local/bin/
 
-      - name: Run pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
-
       - name: Login to Docker Hub
         uses: docker/login-action@v1
         with:
@@ -53,4 +49,8 @@ jobs:
       - name: Build and publish to docker
         run: |
           docker build  --platform linux/amd64 -t adamd3/bactseq:latest .
-          docker push adamd3/bactseq:latest
\ No newline at end of file
+          docker push adamd3/bactseq:latest
+          
+      - name: Run pipeline with test data
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
\ No newline at end of file

From 833e58ada91f55a90d9a3d10a70208ce0238cd76 Mon Sep 17 00:00:00 2001
From: Adam Dinan <adam1989ie@gmail.com>
Date: Wed, 12 Jun 2024 20:06:44 +0100
Subject: [PATCH 2/2] Install env in Dockerfile

---
 Dockerfile | 38 ++++++++++----------------------------
 1 file changed, 10 insertions(+), 28 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index b931000..8deeac0 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,35 +1,17 @@
-FROM ubuntu:22.04
+FROM continuumio/miniconda3
 LABEL maintainer="Adam Dinan <ad866@cam.ac.uk>"
 
-ARG DEBIAN_FRONTEND=noninteractive
+WORKDIR /app
 
-ENV PYTHON_VERSION=3.8.5
+COPY environment.yml .
 
-ADD https://raw.githubusercontent.com/adamd3/BactSeq/main/requirements.txt .
+RUN conda env create -f environment.yml
 
-COPY requirements.txt /tmp
-WORKDIR /tmp
+RUN echo "source activate $(grep -m 1 -E 'name: *' environment.yml | cut -d' ' -f2)" \
+    > ~/.bashrc
 
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ca-certificates  \
-    build-essential \
-    curl libssl-dev libcurl4-openssl-dev libxml2-dev libfontconfig1-dev \
-    python3-numpy python3-pip gawk pigz r-base-dev fastqc \
-    trim-galore samtools bwa kallisto && \
-    apt-get clean autoclean
+SHELL ["conda", "run", "-n", \
+    "$(grep -m 1 -E 'name: *' environment.yml | cut -d' ' -f2)", "/bin/bash", "-c"]
 
-RUN pip install --no-cache-dir -r requirements.txt
-
-RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.rstudio.com'; \
-    options(repos = r);" > ~/.Rprofile
-
-RUN R -e 'install.packages(c(  \
-    "optparse", "fastmap", "RColorBrewer", "reshape2", \
-    "tidyverse", "ape", "scales", "pheatmap", "matrixstats",  \
-    "plyr", "rsqlite", "umap", "xtable", "BiocManager"))'
-
-RUN R -e 'BiocManager::install(c("edgeR", "DESeq2", "GO.db",  \
-    "Rsubread", "topGO"))'
-
-RUN R -e 'if(!require("remotes")) install.packages("remotes"); \
-    remotes::install_github("kevinblighe/EnhancedVolcano")' 
\ No newline at end of file
+# Open a shell by default when the container is run interactively
+ENTRYPOINT ["bash"]