Merge pull request #10 from EichlerLab/main

Update Augustus Dockerfile

docker/augustus/Dockerfile

@@ -1,54 +1,17 @@
-FROM ubuntu:20.04
+FROM continuumio/miniconda3
 
-# Set timezone in tzdata
-ENV DEBIAN_FRONTEND="noninteractive" TZ="Europe/Berlin"
+MAINTAINER Julie Wertz
 
-# Install required packages
-RUN apt-get update
-RUN apt-get install -y build-essential wget git autoconf
+COPY ./environment.yml /
 
-# Install dependencies for AUGUSTUS comparative gene prediction mode (CGP)
-RUN apt-get install -y libgsl-dev libboost-all-dev libsuitesparse-dev liblpsolve55-dev
-RUN apt-get install -y libsqlite3-dev libmysql++-dev
+RUN conda update -n base conda && \
+        conda install -n base conda-libmamba-solver && \
+        conda config --set solver libmamba && \
+        conda env create -f /environment.yml && \
+        conda clean -a
 
-# Install dependencies for the optional support of gzip compressed input files
-RUN apt-get install -y libboost-iostreams-dev zlib1g-dev
+ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/conda/envs/augustus/lib/
 
-# Install dependencies for bam2hints and filterBam
-RUN apt-get install -y libbamtools-dev
-
-# Install additional dependencies for bam2wig
-RUN apt-get install -y samtools libhts-dev
-
-# Install additional dependencies for homGeneMapping and utrrnaseq
-RUN apt-get install -y libboost-all-dev
-
-# Install additional dependencies for scripts
-RUN apt-get install -y cdbfasta diamond-aligner libfile-which-perl libparallel-forkmanager-perl libyaml-perl libdbd-mysql-perl
-RUN apt-get install -y --no-install-recommends python3-biopython
-
-# Install hal - required by homGeneMapping
-# execute the commented out code if you want to use this program - see auxprogs/homGeneMapping/Dockerfile
-#RUN apt-get install -y libhdf5-dev
-#RUN git clone https://github.com/benedictpaten/sonLib.git /opt/sonLib
-#WORKDIR /opt/sonLib
-#RUN make
-#RUN git clone https://github.com/ComparativeGenomicsToolkit/hal.git /opt/hal
-#WORKDIR /opt/hal
-#ENV RANLIB=ranlib
-#RUN make
-#ENV PATH="${PATH}:/opt/hal/bin"
-
-# Clone AUGUSTUS repository
-ADD / /root/augustus
-
-# Build AUGUSTUS
-WORKDIR "/root/augustus"
-RUN make clean
-RUN make
-RUN make install
-ENV PATH="/root/augustus/bin:/root/augustus/scripts:${PATH}"
-
-# Test AUGUSTUS
-RUN make unit_test
+ENV PATH=/opt/conda/envs/augustus/bin/:${PATH}
 
+RUN echo "source activate augustus" > ~/.bashrc

docker/augustus/environment.yml

@@ -0,0 +1,8 @@
+name: augustus
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::augustus
+prefix: /opt/conda/envs/augustus