Merge pull request #5 from Tony-xy-Liu/dev

update master

.dockerignore

@@ -0,0 +1,5 @@
+/*
+!/src
+/src/**/__pycache__
+/src/*.egg-info
+!/envs

.gitignore

@@ -1,5 +1,20 @@
+__pycache__
+
 .idea/
 *_env/
+*.sif
+*.egg-info
 
 tests/test_data/FabFos_DB/
 trim_sequences.fasta.*
+
+/dist
+/build
+/conda_build
+/conda_recipe/*
+!/conda_recipe/compile_recipe.py
+!/conda_recipe/meta_template.yaml
+/data
+/scratch
+/docker/src
+/secrets

Dockerfile

@@ -0,0 +1,41 @@
+ARG CONDA_ENV=fabfos
+
+FROM condaforge/mambaforge as build-env
+# https://mamba.readthedocs.io/en/latest/user_guide/mamba.html
+
+# scope var from global
+ARG CONDA_ENV
+COPY ./envs/base.yml /opt/env.yml
+# Create conda environment:
+# name must match what is in conda.yml
+RUN mamba env create --no-default-packages -n $CONDA_ENV -f /opt/env.yml\
+    && mamba clean -afy
+
+# use a smaller runtime image
+# jammy is ver. 22.04 LTS
+# https://wiki.ubuntu.com/Releases
+FROM ubuntu:jammy
+# scope var from global
+ARG CONDA_ENV
+COPY --from=build-env /opt/conda/envs/${CONDA_ENV} /opt/conda/envs/${CONDA_ENV}
+ENV PATH /opt/conda/envs/${CONDA_ENV}/bin:$PATH
+
+COPY ./src/fabfos /app/fabfos_src
+RUN echo "python -m fabfos_src \$@" >/app/fabfos && chmod +x /app/fabfos
+ENV PATH /app:$PATH
+ENV PYTHONPATH /app:$PYTHONPATH
+
+# Singularity uses tini, but raises warnings
+# we set it up here correctly for singularity
+ENV TINI_VERSION v0.19.0
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
+RUN chmod +x /tini
+
+## We do some umask munging to avoid having to use chmod later on,
+## as it is painfully slow on large directores in Docker.
+RUN old_umask=`umask` && \
+    umask 0000 && \
+    umask $old_umask
+
+# singularity doesn't use the -s flag, and that causes warnings
+ENTRYPOINT ["/tini", "-s", "--"]