enh: update for neurodocker version 0.4.0

Author: Jakub Kaczmarzyk

doc/users/neurodocker.rst

@@ -7,13 +7,11 @@ Neurodocker tutorial
 This page covers the steps to create containers with Neurodocker_.
 
 Neurodocker_ is a command-line program that enables users to generate Docker_
-containers that include neuroimaging software. These containers can be
-converted to Singularity_ containers for use in high-performance computing
-centers.
+containers and Singularity_ images that include neuroimaging software.
 
 Requirements:
 
-* Docker_
+* Docker_ or Singularity_
 * Internet connection
 
 
@@ -22,7 +20,7 @@ Usage
 
 To view the Neurodocker help message
 ::
-    docker run --rm kaczmarj/neurodocker:v0.3.2 generate --help
+    docker run --rm kaczmarj/neurodocker:0.4.0 generate --help
 
 1. Users must specify a base Docker image and the package manager. Any Docker
    image on DockerHub can be used as your base image. Common base images
@@ -37,20 +35,32 @@ To view the Neurodocker help message
    machine into the container, and other operations. The list of supported
    neuroimaging software packages is available in the ``neurodocker`` help
    message.
-3. The ``neurodocker`` command will generate a Dockerfile. This Dockerfile can
-   be used to build a Docker image with the ``docker build`` command.
+3. The ``neurodocker`` command will generate a Dockerfile or Singularity recipe.
+   The Dockerfile can be used with the ``docker build`` command to build a
+   Docker image. The Singularity recipe can be used to build a Singularity
+   container with the ``singularity build`` command.
 
 
-Create a Dockerfile with FSL, Python 3.6, and Nipype
-----------------------------------------------------
+Create a Dockerfile or Singularity recipe with FSL, Python 3.6, and Nipype
+--------------------------------------------------------------------------
 
 This command prints a Dockerfile (the specification for a Docker image) to the
 terminal.
 ::
-  $ docker run --rm kaczmarj/neurodocker:v0.3.2 generate \
+  $ docker run --rm kaczmarj/neurodocker:0.4.0 generate docker \
     --base debian:stretch --pkg-manager apt \
     --fsl version=5.0.10 \
-    --miniconda env_name=neuro \
+    --miniconda create_env=neuro \
+                conda_install="python=3.6 traits" \
+                pip_install="nipype"
+
+This command prints a Singularity recipe (the specification for a Singularity
+container) to the terminal.
+::
+  $ docker run --rm kaczmarj/neurodocker:0.4.0 generate singularity \
+    --base debian:stretch --pkg-manager apt \
+    --fsl version=5.0.10 \
+    --miniconda create_env=neuro \
                 conda_install="python=3.6 traits" \
                 pip_install="nipype"
 
@@ -60,24 +70,38 @@ Build the Docker image
 
 The Dockerfile can be saved and used to build the Docker image
 ::
-  $ docker run --rm kaczmarj/neurodocker:v0.3.2 generate \
+  $ docker run --rm kaczmarj/neurodocker:0.4.0 generate docker \
     --base debian:stretch --pkg-manager apt \
     --fsl version=5.0.10 \
-    --miniconda env_name=neuro \
+    --miniconda create_env=neuro \
                 conda_install="python=3.6 traits" \
                 pip_install="nipype" > Dockerfile
   $ docker build --tag my_image .
   $ # or
   $ docker build --tag my_image - < Dockerfile
 
 
+Build the Singularity container
+-------------------------------
+
+The Singularity recipe can be saved and used to build the Singularity container
+::
+  $ docker run --rm kaczmarj/neurodocker:0.4.0 generate singularity \
+    --base debian:stretch --pkg-manager apt \
+    --fsl version=5.0.10 \
+    --miniconda create_env=neuro \
+                conda_install="python=3.6 traits" \
+                pip_install="nipype" > Singularity
+  $ singularity build Singularity my_nipype.sqsh
+
+
 Use NeuroDebian
 ---------------
 
 This example installs AFNI and ANTs from the NeuroDebian repositories. It also
 installs ``git`` and ``vim``.
 ::
-  $ docker run --rm kaczmarj/neurodocker:v0.3.2 generate \
+  $ docker run --rm kaczmarj/neurodocker:0.4.0 generate [docker|singularity] \
     --base neurodebian:stretch --pkg-manager apt \
     --install afni ants git vim
 
@@ -94,18 +118,18 @@ Create a container with ``dcm2niix``, Nipype, and jupyter notebook. Install
 Miniconda as a non-root user, and activate the Miniconda environment upon
 running the container.
 ::
-  $ docker run --rm kaczmarj/neurodocker:v0.3.2 generate \
+  $ docker run --rm kaczmarj/neurodocker:0.4.0 generate docker \
     --base centos:7 --pkg-manager yum \
     --dcm2niix version=master \
     --user neuro \
-    --miniconda env_name=neuro conda_install="jupyter traits nipype" \
+    --miniconda create_env=neuro conda_install="jupyter traits nipype" \
     > Dockerfile
   $ docker build --tag my_nipype - < Dockerfile
 
 
 Copy local files into a container.
 ::
-  $ docker run --rm kaczmarj/neurodocker:v0.3.2 generate \
+  $ docker run --rm kaczmarj/neurodocker:v0.3.2 generate [docker|singularity] \
     --base ubuntu:16.04 --pkg-manager apt \
     --copy relative/path/to/source.txt /absolute/path/to/destination.txt