Make container compatible with Nextflow and Singularity

 - Add bash to container as Nextflow needs this to do its own business
 - Replace forced ENTRYPOINT with soft CMD for Singularity and Nextflow
   + Note: running the container now needs 'hamronize' as first argument,
     this was previously the implicit (and enforced) ENTRYPOINT
 - Document in README the docker run ... invocation line
 - Remove the (unneeded) licensed Conda 'default' channel in README

Author: zwets

Dockerfile

@@ -15,15 +15,17 @@ LABEL tags="Genomics"
 # maintainer
 MAINTAINER Finlay Maguire <[email protected]>
 
+# add bash so Nextflow can run the container
+RUN apk add --no-cache bash && rm -rf /var/cache/apk/*
+
 # set the working directory in the container
 WORKDIR /hAMRonization
 
 # copy the sources into the container
 COPY . /hAMRonization/src
 
 # install dependencies and clean all up
-RUN python -m pip --no-cache install ./src && rm -rf ./src
+RUN python -m pip --no-cache-dir install ./src && rm -rf ./src
 
-# command to run on container start
-ENTRYPOINT ["hamronize"]
-CMD ["--help"]
+# command to run on container start without args
+CMD ["hamronize", "--help"]

README.md

@@ -19,7 +19,7 @@ This supports a variety of summary options including an [interactive summary](ht
 
 ## Installation
 
-This tool requires python>=3.7 and [pandas](https://pandas.pydata.org/)
+This tool requires python>=3.9 and [pandas](https://pandas.pydata.org/)
 and the latest release can be installed directly from pip, conda, docker, this repository, or from the galaxy toolshed:
 ```
 pip install hAMRonization
@@ -30,16 +30,17 @@ pip install hAMRonization
 Or
 
 ```
-conda create --name hamronization --channel conda-forge --channel bioconda --channel defaults hamronization
+conda create --name hamronization --channel conda-forge --channel bioconda hamronization
 ```
 ![version-on-conda](https://anaconda.org/bioconda/hamronization/badges/version.svg)
 ![conda-download](https://anaconda.org/bioconda/hamronization/badges/downloads.svg)
 ![last-update-on-conda](https://anaconda.org/bioconda/hamronization/badges/latest_release_date.svg)
 
 
-Or to install using docker:
+Or to install and run using docker, podman, singularity:
 ```
-docker pull finlaymaguire/hamronization:latest
+docker pull docker.io/finlaymaguire/hamronization:latest
+docker run --rm docker.io/finlaymaguire/hamronization:latest hamronize --help
 ```
 
 Or to install the latest development version: