Merge pull request #30 from cfe-lab/introduce-docker

Introduce docker

.github/workflows/python-app.yml

@@ -29,3 +29,14 @@ jobs:
     - name: Test with pytest
       run: |
         pipenv run python -m pytest
+
+  docker-build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Build docker image
+      run: docker build -t proviral .
+    - name: Run the image
+      run: docker run --rm proviral --help

Dockerfile

@@ -0,0 +1,12 @@
+
+FROM ubuntu:22.04
+
+ENV LANG=en_US.UTF-8
+
+COPY setup.py     /opt/primer_finder/setup.py
+COPY gene_splicer /opt/primer_finder/gene_splicer/
+COPY scripts      /opt/primer_finder/scripts/
+
+RUN sh -- /opt/primer_finder/scripts/install.sh
+
+ENTRYPOINT ["gene_splicer_sample", "--hivseqinr", "/opt/hivseqinr"]

Singularity

@@ -20,37 +20,10 @@ From: ubuntu:22.04
 %files
     setup.py /opt/primer_finder/
     gene_splicer /opt/primer_finder/
+    scripts /opt/primer_finder/
 
 %post
-    echo ===== Installing Prerequisites ===== >/dev/null
-    apt-get update
-    apt-get install -y build-essential unzip git wget \
-        fontconfig libbz2-dev liblzma-dev libssl-dev \
-        libffi-dev libsqlite3-dev
-
-    echo ===== Installing Python ===== >/dev/null
-    apt-get install -y python3 python3-pip
-
-    echo ===== Installing blast ===== >/dev/null
-    apt-get install -y ncbi-blast+
-
-    echo ===== Installing Python packages ===== >/dev/null
-    cd /opt/primer_finder
-    pip3 install .
-
-    echo ===== Installing minimap2 ===== >/dev/null
-    apt-get install -y minimap2
-
-    echo ===== Installing hivseqinr ===== >/dev/null
-    apt-get install -y libz-dev libcurl4-openssl-dev libxml2-dev
-    DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y r-base
-    Rscript /opt/primer_finder/gene_splicer/configure_r.sh
-    python3 -m gene_splicer.hivseqinr /opt/hivseqinr
-
-    # Clean up
-    apt-get remove -y wget git build-essential
-    apt-get clean
-    rm -rf /var/lib/apt/lists/*
+    sh -- /opt/primer_finder/scripts/install.sh
 
 %environment
     export LANG=en_US.UTF-8

scripts/install.sh

@@ -0,0 +1,12 @@
+#! /bin/sh
+
+set -e
+
+CURRENT_DIR="${0%/*}"
+
+set -x
+
+for SCRIPT in "$CURRENT_DIR/installation/"*
+do
+    sh -- "$SCRIPT"
+done

scripts/installation/10-prerequisites.sh

@@ -0,0 +1,12 @@
+#! /bin/sh
+
+set -e
+
+echo ===== Installing Prerequisites ===== >/dev/null
+
+set -x
+
+apt-get update -qq
+apt-get install -y build-essential unzip git wget \
+        fontconfig libbz2-dev liblzma-dev libssl-dev \
+        libffi-dev libsqlite3-dev

scripts/installation/15-python.sh

@@ -0,0 +1,9 @@
+#! /bin/sh
+
+set -e
+
+echo ===== Installing Python ===== >/dev/null
+
+set -x
+
+apt-get install -y python3 python3-pip

scripts/installation/20-blast.sh

@@ -0,0 +1,9 @@
+#! /bin/sh
+
+set -e
+
+echo ===== Installing blast ===== >/dev/null
+
+set -x
+
+apt-get install -y ncbi-blast+

scripts/installation/25-python-packages.sh

@@ -0,0 +1,9 @@
+#! /bin/sh
+
+set -e
+
+echo ===== Installing Python packages ===== >/dev/null
+
+set -x
+
+pip3 install /opt/primer_finder

scripts/installation/30-minimap2.sh

@@ -0,0 +1,9 @@
+#! /bin/sh
+
+set -e
+
+echo ===== Installing minimap2 ===== >/dev/null
+
+set -x
+
+apt-get install -y minimap2

scripts/installation/35-hivseqinr.sh

@@ -0,0 +1,14 @@
+#! /bin/sh
+
+set -e
+
+echo ===== Installing hivseqinr ===== >/dev/null
+
+set -x
+
+export DEBIAN_FRONTEND=noninteractive
+
+apt-get install -y libz-dev libcurl4-openssl-dev libxml2-dev
+apt-get install --no-install-recommends -y r-base
+Rscript /opt/primer_finder/gene_splicer/configure_r.sh
+python3 -m gene_splicer.hivseqinr /opt/hivseqinr

scripts/installation/90-cleanup.sh

@@ -0,0 +1,11 @@
+#! /bin/sh
+
+set -e
+
+echo ===== Clean up ===== >/dev/null
+
+set -x
+
+apt-get remove -y wget git build-essential
+apt-get clean
+rm -rf /var/lib/apt/lists/*