Snakemake

Dockerfile

@@ -1,96 +1,49 @@
-FROM ubuntu:16.04
+FROM continuumio/anaconda3:2020.07
+
 MAINTAINER Tomaz Curk <tomazc@gmail.com>
 
+# suppress prompt for tzdata
+ENV DEBIAN_FRONTEND=noninteractive
+ENV TZ=Europe/Ljubljana
+
 # thanks to https://github.com/bschiffthaler/ngs/blob/master/base/Dockerfile
 # and https://github.com/AveraSD/ngs-docker-star/blob/master/Dockerfile
 
-RUN useradd -m -d /home/icuser icuser
-
-# update system
-RUN sed -Ei 's/^# deb-src /deb-src /' /etc/apt/sources.list
-RUN apt-get update && apt-get upgrade -y && \
-    apt-get install -y \
-    build-essential \
-    gfortran \
-    libatlas-base-dev \
-    wget \
-    g++ \
-    make \
-    binutils \
-    python3 \
-    python3-pip \
-    python3-setuptools \
-    python-virtualenv \
-    python-pip \
-    pandoc \
-    git && \
-    apt-get build-dep -y python3-matplotlib
-
-RUN apt-get autoclean -y && \
-    apt-get autoremove -y
+RUN apt-get install -y vim
+RUN apt-get install -y nano
 
+SHELL ["/bin/bash", "--login", "-c"]
 
-#################
-### samtools
-RUN apt-get install -y \
-    zlib1g-dev \
-    liblzma-dev \
-    libbz2-dev \
-    samtools
+RUN conda update -n base -c defaults conda -y
+RUN conda install -c conda-forge mamba -y
 
+RUN conda config --add channels defaults
+RUN conda config --add channels bioconda
+RUN conda config --add channels conda-forge
 
 #################
-### bedtools, need at least version 2.26, where merge command reports strand
-# RUN apt-get install -y bedtools
-WORKDIR /tmp/bedtools
-RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz
-RUN tar -zxvf bedtools-2.27.1.tar.gz
-WORKDIR /tmp/bedtools/bedtools2
-RUN make
-RUN make install
-WORKDIR /tmp
-RUN rm -rfv bedtools
-
+#### iCount
 #################
-### RNA-star
-WORKDIR /tmp/STAR
-RUN wget https://github.com/alexdobin/STAR/archive/2.6.1a.tar.gz
-RUN tar -xvzf 2.6.1a.tar.gz
-WORKDIR /tmp/STAR/STAR-2.6.1a/source
-RUN make STAR
-RUN mkdir -p /home/icuser/bin && cp STAR /home/icuser/bin
-WORKDIR /tmp
-RUN rm -rfv STAR
-
 
-#################
-#### iCount
+RUN useradd -m -d /home/icuser icuser
+ADD . /home/icuser/iCount
 RUN chown -R icuser.icuser /home/icuser
 
 USER icuser
 WORKDIR /home/icuser
-RUN virtualenv -p python3 /home/icuser/.icountenv
-
-USER root
-# to speed-up building of Docker images
-RUN /home/icuser/.icountenv/bin/pip install numpy pandas pysam pybedtools numpydoc matplotlib
-
-ADD . /home/icuser/iCount_src
-RUN chown -R icuser.icuser /home/icuser
+RUN mkdir /home/icuser/storage
 
-USER icuser
-WORKDIR /home/icuser/iCount_src
+RUN conda create -c conda-forge -c bioconda -n iCount_pipeline3 -y
+RUN conda init bash
+RUN echo "conda activate iCount_pipeline3" >> ~/.bashrc
 
-RUN ../.icountenv/bin/pip install -e .[docs,test]
+SHELL ["conda", "run", "-n", "iCount_pipeline3", "/bin/bash", "-c"]
 
-USER root
-RUN echo "source /home/icuser/.icountenv/bin/activate" >> /etc/bash.bashrc
-USER icuser
+### needs ~ 4 GB RAM, otherwise killed
+RUN conda env update --file iCount/conda_iCount.yaml
 
-RUN mkdir /home/icuser/storage
+RUN pip install ./iCount
 
 ENV PATH /home/icuser/bin:$PATH
-
 WORKDIR /home/icuser
-
 CMD ["/bin/bash"]

conda_iCount.yaml

@@ -0,0 +1,27 @@
+channels:
+  - defaults
+  - bioconda
+  - conda-forge
+
+dependencies:
+  - python = 3.8.6
+  - snakemake = 5.32.2
+  - jinja2 = 2.11.2
+  - networkx = 2.5
+  - bcftools = 1.11
+  - samtools = 1.11
+  - bwa = 0.7.17
+  - pysam = 0.16.0.1
+  - cutadapt = 3.0
+  - bedtools = 2.29.2
+  - STAR = 2.7.6a
+  - trim-galore = 0.6.6
+  - pip = 20.2.4
+  - pybedtools = 0.8.1
+  - numpy = 1.19.4
+  - pandas = 1.1.4
+  - numpydoc = 1.1.0
+  - sphinx = 3.3.1
+  - matplotlib = 3.3.3
+  - docutils = 0.16
+  - sphinx-releases = 1.6.1