Merge pull request #2 from johnegarza/add_dockerfile

Add dockerfile

Dockerfile

@@ -0,0 +1,47 @@
+FROM ubuntu:bionic
+# AGFusion original source code is available at https://github.com/murphycj/AGFusion
+# This docker image was originally derived from rachelbj/agfusion:1.1
+
+
+# INSTALL DEPENDENCIES
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV PYENSEMBL_CACHE_DIR=/opt
+
+RUN apt-get update -y
+RUN apt-get install -y build-essential python3 python3-pip python3-matplotlib python3-pandas python3-future python3-biopython curl less vim libnss-sss git
+RUN pip3 install pyensembl
+
+# Additional libraries needed for AGFusion build command
+RUN apt-get install -y default-libmysqlclient-dev
+RUN pip3 install mysqlclient
+
+
+# INSTALL AGFUSION & DATABASE FILES
+
+ENV ensembl_version=95
+
+# Download latest AGFusion from source and install with pip
+WORKDIR /usr/local/bin
+RUN git clone https://github.com/genome/AGFusion.git
+WORKDIR /usr/local/bin/AGFusion
+RUN pip3 install .
+
+# Install AGFusion databases
+RUN mkdir -p /opt/agfusiondb/
+WORKDIR /opt/agfusiondb
+# Pre-generated db files are available for ensembl_version < 93 and can be downloaded using:
+# RUN agfusion download -s homo_sapiens -r ${ensembl_version} -d /opt/agfusiondb/
+# RUN agfusion download -s mus_musculus -r ${ensembl_version} -d /opt/agfusiondb/
+# To use newer versions, the db must be built from source with the follow commands:
+# At the time of writing, this downloads Pfam release 35
+RUN curl http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/database_files/pfamA.txt.gz > pfamA.txt.gz
+RUN gunzip pfamA.txt.gz
+RUN agfusion build --dir . --species homo_sapiens --release ${ensembl_version} --pfam pfamA.txt
+RUN agfusion build --dir . --species mus_musculus --release ${ensembl_version} --pfam pfamA.txt
+RUN rm pfamA.txt
+
+# Install pyensembl databases
+RUN pyensembl install --species homo_sapiens --release ${ensembl_version}
+RUN pyensembl install --species mus_musculus --release ${ensembl_version}
+