Merge pull request #117 from arnaudbore/add_container

Add containers

CHANGELOG.md

@@ -1,9 +1,14 @@
 # CHANGELOG
 
+## 2.1.6 - 2021-02-16
+
+- New Containers
+- Fix pypi package
+
 ## 2.1.5 - 2021-01-04
 
 - Add possibility to be not case sensitive
-- Fix issue 34: dcm2bids not ordering runs chronologically 
+- Fix issue 34: dcm2bids not ordering runs chronologically
 
 ## 2.1.4 - 2019-04-04
 

containers/Dockerfile

@@ -0,0 +1,26 @@
+From ubuntu:latest
+ENV DEBIAN_FRONTEND=noninteractive
+
+MAINTAINER Arnaud Boré <[email protected]>
+
+RUN apt-get update
+RUN apt-get -y upgrade
+
+RUN apt-get -y install wget build-essential cmake git pigz \
+               nodejs python3 python3-pip unzip
+
+RUN pip3 install dcm2bids
+
+# Install dcm2niix from github
+ENV DCM2NIIX_VERSION="v1.0.20201102"
+
+WORKDIR /usr/local/src
+RUN git clone https://github.com/rordenlab/dcm2niix.git
+WORKDIR /usr/local/src/dcm2niix
+RUN git checkout tags/${DCM2NIIX_VERSION} -b install
+RUN mkdir build
+WORKDIR /usr/local/src/dcm2niix/build
+RUN cmake ..
+RUN make install
+
+WORKDIR /

containers/singularity.def

@@ -0,0 +1,2 @@
+BootStrap: docker
+From: unfmontreal/dcm2bids:latest

dcm2bids/version.py

@@ -3,7 +3,7 @@
 """This module take care of the versioning"""
 
 # dcm2bids version
-__version__ = "2.1.5"
+__version__ = "2.1.6"
 
 
 import logging

docs/1-usage.md

@@ -51,3 +51,19 @@ To build the configuration file, you need to have a example of the sidecars. You
 Create basic BIDS files and directories in the output directory (by default folder where the script is launched).
 
 [json-editor]: http://jsoneditoronline.org/
+
+
+# Containers
+
+You can also use all the tools through docker or singularity images.
+
+## Docker
+Download the latest release of the Docker container for dcm2bids:
+
+`docker pull unfmontreal/dcm2bids:latest`
+
+## Singularity
+
+Build the latest singularity image:
+
+`singularity build dcm2bids.sif containers/singularity.def`