feat: create Dockerfile based on bioconda recipe

deps listed here: https://github.com/bioconda/bioconda-recipes/blob/e4f33b5c94119efef67e6da9955f458c29ab40d9/recipes/mimseq/meta.yaml
CCBR · Nov 7, 2023 · 717b17d · 717b17d
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diff --git a/.github/workflows/build-docker.yml b/.github/workflows/build-docker.yml
@@ -0,0 +1,41 @@
+name: build-docker
+
+on:
+  push:
+    branches:
+      - "docker**"
+    paths:
+      - .github/workflows/build-docker.yml
+      - Dockerfile
+      - mimseq/version.py
+
+env:
+  dockerfile: "Dockerfile"
+  namespace: "nciccbr"
+  image_name: "tranquil_mimseq"
+  push: "true"
+
+jobs:
+  build-docker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Login to DockerHub
+        if: ${{ env.push == 'true' }}
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Prepare build-time variables
+        id: vars
+        run: |
+            echo "VERSION=$( cat mimseq/version.py | grep -oP 'v(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?' )"  >> "$GITHUB_OUTPUT"
+            echo "CONTEXT=$(dirname ${{ env.dockerfile }})" >> "$GITHUB_OUTPUT"
+            echo "DATE=$(date +"%Y-%m-%d")" >> "$GITHUB_OUTPUT"
+      - name: Build and push
+        uses: docker/build-push-action@v4
+        with:
+          context: ${{ steps.vars.outputs.CONTEXT }}
+          file: ${{ env.dockerfile }}
+          push: ${{ env.push }}
+          tags: ${{ env.namespace }}/${{ env.image_name }}:${{ steps.vars.outputs.VERSION }}
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,90 @@
+FROM python:3.7.17-bookworm
+
+RUN mkdir -p /opt2 && mkdir -p /data2
+ENV TZ=America/New_York
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+
+RUN apt update && apt-get -y upgrade
+# Set the locale
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+		locales build-essential cmake cpanminus && \
+	localedef -i en_US -f UTF-8 en_US.UTF-8 && \
+	cpanm FindBin Term::ReadLine
+
+RUN apt-get update && apt-get install -y \
+	curl \
+  libffi-dev \
+  libdeflate-dev \
+  libsqlite3-dev \
+  libcurl4-openssl-dev \
+	pigz \
+	unzip \
+  wget
+
+# Install conda and give write permissions to conda folder
+RUN echo 'export PATH=/opt2/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
+    wget --quiet "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O ~/miniforge3.sh && \
+    /bin/bash ~/miniforge3.sh -b -p /opt2/conda && \
+    rm ~/miniforge3.sh && chmod 777 -R /opt2/conda/
+
+# install most mimseq deps from conda
+RUN mamba install \
+    python=3.7 \
+    'r-base>=4.1' \
+    'biopython>=1.79' \
+    'matplotlib-base>=3.4.2' \
+    'numpy>=1.21.1' \
+    'pandas>=1.3.1' \
+    'requests>=2.26.0' \
+    'pybedtools>=0.8.2' \
+    'pyfiglet>=0.8.post1' \
+    'pysam>=0.16.0.1' \
+    'seaborn-base>=0.11.1' \
+    'statsmodels>=0.13.1' \
+    'infernal>=1.1.4' \
+    'blast>=2.10.1' \
+    'gmap<=2019.02.26' \
+    'samtools>=1.11' \
+    'bedtools>=2.30.0' \
+    'r-ggplot2>=3.3.5' \
+    'r-ggpol>=0.0.7' \
+    'bioconductor-complexheatmap>=2.2.0' \
+    'bioconductor-deseq2>=1.26.0' \
+    'r-pheatmap>=1.0.12' \
+    'r-calibrate>=1.7.7' \
+    'r-gridextra>=2.3' \
+    'r-plyr>=1.8.6' \
+    'r-dplyr>=1.0.6' \
+    'r-tidyverse>=1.3.0' \
+    'r-devtools>=2.4.1' \
+    'r-reshape2>=1.4.4' \
+
+# install usearch
+RUN wget https://drive5.com/downloads/usearch10.0.240_i86linux32.gz && \
+        gunzip usearch10.0.240_i86linux32.gz && \
+        chmod a+x usearch10.0.240_i86linux32 && \
+        mkdir -p /opt2/usearch && \
+        mv usearch10.0.240_i86linux32 /opt2/usearch/usearch && \
+        rm -f usearch10.0.240_i86linux32.gz
+ENV PATH=/opt2/usearch:$PATH
+
+# install local mimseq
+COPY . /opt2/mim-tRNAseq
+WORKDIR /opt2/mim-tRNAseq
+RUN pip install --upgrade pip && \
+  pip install . && \
+  mimseq --version
+
+# check mimseq installation
+WORKDIR /opt2
+RUN which mimseq && mimseq --version
+RUN python --version
+
+# cleanup
+RUN apt-get clean && apt-get purge && \
+  rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* 
+
+COPY Dockerfile /opt2/Dockerfile
+RUN chmod -R a+rX /opt2/Dockerfile
+
+WORKDIR /data2