From 3901673eb46e0608dd88db4278c72f76e6df6ad5 Mon Sep 17 00:00:00 2001
From: Alex Kanitz <alexander.kanitz@alumni.ethz.ch>
Date: Thu, 19 May 2022 12:37:10 +0200
Subject: [PATCH] build: add Dockerfile (#80)

---
 .dockerignore |  8 ++++++++
 Dockerfile    | 44 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+)
 create mode 100644 .dockerignore
 create mode 100644 Dockerfile

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 00000000..2de06c86
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,8 @@
+*
+!data/
+!htsinfer/
+!tests/
+!setup.py
+!environment.yml
+!LICENSE
+!README.md
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 00000000..36deb869
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,44 @@
+###### BASE IMAGE ######
+FROM continuumio/miniconda3:4.11.0
+
+####### METADATA #######
+LABEL base_image="continuumio/miniconda3:4.11.0"
+LABEL version="1.0"
+LABEL software="HTSinfer"
+LABEL software.version="v0.9.0"
+LABEL about.summary="HTSinfer infers metadata from High Throughput Sequencing (HTS) data"
+LABEL about.home="https://github.com/zavolanlab/htsinfer"
+LABEL about.documentation="https://htsinfer.readthedocs.io/"
+LABEL about.license_file="https://spdx.org/licenses/Apache-2.0"
+LABEL about.license="Apache License 2.0"
+LABEL about.tags="bioinformatics, ngs"
+
+###### MAINTAINER ######
+LABEL maintainer="Alexander Kanitz <alexander.kanitz@alumni.ethz.ch>"
+LABEL maintainer.organisation="Biozentrum, University of Basel"
+LABEL maintainer.location="Spitalstrasse 41, CH-4056 Basel, Switzerland"
+LABEL maintainer.lab="Zavolan Lab"
+
+##### INSTALLATION #####
+
+# COPY THE YAML & INSTALL SOFTWARE WITH CONDA
+WORKDIR /usr/src/app
+COPY ./ ./
+RUN conda env create --file environment.yml \
+    && conda clean --all
+
+# VARIABLES
+ARG WORKDIR="/home/USER"
+ARG USER="USER"
+ARG GROUP="GROUP"
+ENV PATH="${WORKDIR}:${PATH}"
+
+# CREATE USER
+RUN groupadd -r ${GROUP} && useradd --no-log-init -r -g ${GROUP} ${USER}
+
+# SET ENVIRONMENT
+WORKDIR ${WORKDIR}
+RUN chown -R ${USER}:${GROUP} ${WORKDIR} && chmod 700 ${WORKDIR}
+USER ${USER}
+RUN echo "source activate htsinfer" > ~/.bashrc
+ENV PATH /opt/conda/envs/htsinfer/bin:$PATH