From 1282878f0f3b6d6fd306139751453ddd6166cba3 Mon Sep 17 00:00:00 2001
From: Chris Flerin <ccflerin@gmail.com>
Date: Thu, 1 Apr 2021 17:04:21 +0200
Subject: [PATCH] Update single_cell_toolkit Docker image - Use zlib-ng base
 image (#325) - Include saturation script (#332), and python 3.7 install

---
 src/singlecelltoolkit/Dockerfile | 63 +++++++++++---------------------
 1 file changed, 22 insertions(+), 41 deletions(-)

diff --git a/src/singlecelltoolkit/Dockerfile b/src/singlecelltoolkit/Dockerfile
index f5b2d519..d709a38b 100644
--- a/src/singlecelltoolkit/Dockerfile
+++ b/src/singlecelltoolkit/Dockerfile
@@ -1,39 +1,26 @@
-FROM ubuntu:20.04
+FROM vibsinglecellnf/samtools:1.12
 
 ENV DEBIAN_FRONTEND=noninteractive
-RUN BUILDPKGS="autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev \
-    git \
-    libhts-dev \
-    curl \
-    wget" && \
-    apt-get update && \
-    apt-get install -y apt-utils debconf locales locales-all ca-certificates && dpkg-reconfigure locales && \
-    apt-get install -y --no-install-recommends $BUILDPKGS && \
-    apt-get install -y --no-install-recommends clang python3 llvm-6.0 pigz
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        python3 \
+        python3-venv \
+        wget && \
+        update-alternatives --install /usr/bin/python python /usr/bin/python3.7 100
 
-# install htslib
-ENV HTSLIB_VERSION 1.11
-RUN curl -L -o /tmp/htslib-${HTSLIB_VERSION}.tar.bz2 \
-        https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2 && \
-    mkdir -p /tmp/htslib-${HTSLIB_VERSION} && \
-    tar jxvf /tmp/htslib-${HTSLIB_VERSION}.tar.bz2 -C /tmp/htslib-${HTSLIB_VERSION} --strip-components 1 && \
-    cd /tmp/htslib-${HTSLIB_VERSION} && \
-    ./configure && \
-    make && \
-    make install && \
-    cd .. && rm -rf htslib-${HTSLIB_VERSION}
+RUN python -m venv /opt/venv
+# Make sure we use the virtualenv:
+ENV PATH="/opt/venv/bin:$PATH"
 
-# install samtools
-ENV SAMTOOLS_VERSION 1.11
-RUN curl -L -o /tmp/samtools-${SAMTOOLS_VERSION}.tar.bz2 \
-        https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
-    mkdir -p /tmp/samtools-${SAMTOOLS_VERSION} && \
-    tar jxvf /tmp/samtools-${SAMTOOLS_VERSION}.tar.bz2 -C /tmp/samtools-${SAMTOOLS_VERSION} --strip-components 1 && \
-    cd /tmp/samtools-${SAMTOOLS_VERSION} && \
-    ./configure && \
-    make && \
-    make install && \
-    cd .. && rm -rf samtools-${SAMTOOLS_VERSION}
+RUN pip install --no-cache-dir --upgrade pip wheel && \
+    pip install --no-cache-dir \
+        pandas \
+        scipy \
+        uncertainties \
+        typing \
+        pathlib \
+        matplotlib \
+        numpy
 
 # install seq (https://github.com/seq-lang/seq/):
 ENV SEQ_VERSION=0.9.11
@@ -51,13 +38,7 @@ RUN git clone --depth=1 https://github.com/aertslab/single_cell_toolkit.git /opt
 ENV seq_root_dir=/opt/seq
 ENV PATH="/opt/single_cell_toolkit:${PATH}"
 
-# final set of packages for usability
-RUN apt-get -y update && \
-    apt-get -y --no-install-recommends install \
-        procps \
-        bash-completion \
-        less && \
-    apt-get remove --purge -y $BUILDPKGS && \
-    rm -rf /var/cache/apt/* && \
-    rm -rf /var/lib/apt/lists/*
+RUN rm -rf /var/cache/apt/* && \
+    rm -rf /var/lib/apt/lists/* && \
+    ldconfig