From 579586a5f6c11675f82e5506129ede0d75d7a26c Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 16 Nov 2021 17:01:39 -0600
Subject: [PATCH] Add building (not running yet) Dockerfile

Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
---
 Dockerfile | 115 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 115 insertions(+)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..52f74a0
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,115 @@
+FROM alpine:3.14.3
+
+ARG NANOSIM_VERSION=3.0.2
+ARG MINIMAP2_VERSION=2.18
+ARG LAST_VERSION=916
+ARG LAST_SHA="98fc3d382ef443b4468b633d2fe90ac3d0b3c21e"
+ARG SAMTOOLS_VERSION=1.12
+ARG GENOMETOOLS_VERSION=1.6.2
+
+RUN \
+  # Install real dependencies
+  apk add --repository http://dl-cdn.alpinelinux.org/alpine/edge/main \
+  --update --no-cache \
+    bash \
+    libbz2 \
+    ncurses \
+    py3-pip \
+    python3 \
+    xz \
+    zlib && \
+\
+  # Install build dependencies
+  apk add --repository http://dl-cdn.alpinelinux.org/alpine/edge/main \
+    --no-cache --virtual .build-deps \
+    blas-dev \
+    build-base \
+    bzip2-dev \
+    freetype-dev \
+    g++ \
+    gcc \
+    gfortran \
+    git \
+    lapack-dev \
+    libgfortran \
+    libpng-dev \
+    make \
+    musl-dev \
+    ncurses-dev \
+    openblas-dev \
+    py-pip \
+    python3-dev \
+    wget \
+    xz-dev \
+    zlib-dev &&\
+\
+  # Make python3 the default
+  ln -fs /usr/include/locale.h /usr/include/xlocale.h && \
+  ln -fs /usr/bin/python3 /usr/local/bin/python && \
+  ln -fs /usr/bin/pip3 /usr/local/bin/pip && \
+\
+  # Download and install Minimap2
+  cd /tmp && \
+  wget -qO- https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VERSION}/minimap2-${MINIMAP2_VERSION}.tar.bz2 | tar xjv && \
+  cd minimap2-${MINIMAP2_VERSION} && \
+  make && \
+  cp minimap2 /usr/bin && \
+  mkdir /usr/man && \
+  cp minimap2.1 /usr/man && \
+  cd .. && \
+  rm -rf minimap2-${MINIMAP2_VERSION} && \
+  cd && \
+\
+  # Download and install LAST
+  cd /tmp && \
+  git clone https://gitlab.com/mcfrith/last.git && \
+  cd last && \
+  git checkout ${LAST_SHA} && \
+  make && make install && \
+  cd .. && \
+  rm -rf last && \
+  cd && \
+\
+  # Download and install samtools
+  cd /tmp && \
+  wget https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2 && \
+  tar xjvf samtools-$SAMTOOLS_VERSION.tar.bz2 && \
+  cd samtools-$SAMTOOLS_VERSION && \
+  ./configure && \
+  make && make install && \
+  cd .. && \
+  rm -rf samtools-$SAMTOOLS_VERSION* && \
+  cd && \
+\
+  # Download and install GenomeTools
+  cd /tmp && \
+  wget -qO- https://github.com/genometools/genometools/archive/refs/tags/v${GENOMETOOLS_VERSION}.tar.gz | tar xzv && \
+  cd genometools-${GENOMETOOLS_VERSION} && \
+  make cairo=no errorcheck=no && make cairo=no errorcheck=no install && \
+  cd .. && \
+  rm -rf v${GENOMETOOLS_VERSION} && \
+  cd && \
+\
+  # Download and install Python packages
+  pip3 install -v --no-cache-dir six==1.16.0 && \
+  pip3 install -v --no-cache-dir joblib==0.14.1 && \
+  pip3 install -v --no-cache-dir threadpoolctl && \
+  pip3 install -v --no-cache-dir numpy==1.17.2 && \
+  pip3 install -v --no-cache-dir scipy && \
+  pip3 install -v --no-cache-dir cython && \
+  pip3 install -v --no-cache-dir scikit-learn==0.21.3 && \
+  pip3 install -v --no-cache-dir pysam==0.17 && \
+  pip3 install -v --no-cache-dir HTSeq==0.11.2 && \
+  pip3 install -v --no-cache-dir pybedtools==0.8.2 && \
+\
+  # Download and install NanoSim
+  cd /tmp && \
+  wget -qO- https://github.com/bcgsc/NanoSim/archive/refs/tags/v${NANOSIM_VERSION}.tar.gz | tar xzv && \
+  cd NanoSim-${NANOSIM_VERSION} && \
+  cp -r src/* /usr/bin && \
+  cd .. && \
+  rm -rf NanoSim-${NANOSIM_VERSION} && \
+  cd .. && \
+\
+  # Cleanup build packages
+  apk del --no-cache .build-deps