Neurodocker Versions Save

Additions

• Adds the nd_freeze utility for (Neuro)Debian base images. This allows users to pin the apt sources to a particular date and time and is very useful in creating reproducible builds. Otherwise, calls to apt-get update make builds non-deterministic (#240).

Fixes

• Wraps pip and conda packages in single quotes. This prevents the execution of shell commands like > in numpy>=1.10 (#239).

Additions

• Ability to output JSON representation of the neurodocker specification
• exclude_paths option in FSL to exclude specific paths from tarball extraction
• Python 3.7 support

Fixes

• Install shared libraries required for matlab compiler runtime 2010a
• Add back in nlopt dependency in afni
• PATH variable in afni

Enhancements

• Allows use of miniconda base environment (--miniconda use_env=base ...
• Adds ANTs versions 2.3.1 and 2.3.1, statically compiled on CentOS 6
• Adds matlab compiler runtime 2018b
• Misc. improvements to the reprozip trace wrapper shell script
• Installs desktop manager when installing VNC
• Raises more specific error on dockerfile / singularity recipe generation

This release includes various fixes, enhancements, and additions.

Additions

• vnc command-line option. This installs a VNC server in the container, and optionally starts it at container runtime.
• mrtrix3 source installation

Fixes

• $PATH variable is set properly in neurodocker generate singularity.
• apt_opts="" and yum_opts="" now remove all options in apt-get install and yum install except for -y.
• allow conda environments built from yaml file to be activated at container runtime.

Enhancements

• Improvements in error-handling in neurodocker reprozip trace.
• mrtrix3 binaries are pre-built on centos 6.
• update nipype tutorial example

We are happy to introduce Neurodocker version 0.4.0. This release includes an entirely rewritten core and support for generating Singularity recipes.

As always, if you run into problems using Neurodocker, please submit an issue.

Breaking changes

• CLI for generate commands follows the syntax neurodocker generate [docker|singularity].
• FreeSurfer license file option is removed. License files should be added at container runtime.
• --spm becomes --spm12.
• --miniconda signature has been changed to use create_env and use_env in lieu of env_name.

Additions

• Singularity recipe generation
• Matlab Compiler Runtime can be installed independently of SPM12
• Larger suite of examples

Enhancements

• Software installation instructions are written in a templating language
• Matlab Compiler Runtime URLs use HTTPS.

This is the second release candidate for neurodocker version 0.4.0.

Fixes

• pip installation (previously, the required yaml files were not being installed).
• matlab compiler runtime uses https urls
• documentation is fixed and all examples are functional
• examples are updated to new command line interface

Adds

• --run-bash command line option

Users of this release may notice that features may be have dropped while converting from the old class-based to the new template-based framework. This is not intentional in most cases, so please submit an issue if a feature that you use has been lost.

This is the first release candidate for neurodocker version 0.4.0, which adds support for generating Singularity recipes (and involves a near complete rewrite of neurodocker).

Dockerfiles and Singularity files are generated from templates of installation instructions.

Users of this release may notice that features may be have dropped while converting from the old class-based to the new template-based framework. This is not intentional in most cases, so please submit an issue if a feature that you use has been lost.

Additions

• Singularity recipes can now be generated.
• Matlab Compiler Runtime can be installed independently.

Breaking changes

• CLI for generate commands follows the syntax neurodocker generate docker/singularity
• FreeSurfer license file option is removed. License files should be added at container runtime.
• --spm becomes --spm12

Fixes

• SPM12 takes a specific version release now and does not install dev unless the user requests it.

Changes:

• Adds dcm2niix.
• Replaces option add_to_path with activate in Miniconda installation. activate=True will activate the environment in the entrypoint of the container.
• Makes R installation optional for AFNI.
• Adds option to install Python for AFNI.
• Adds examples.

Changes:

• Installs shared libraries for FSL on apt and yum.
• Allows creation of conda environment from YAML file.
• Adds support for FSL eddy 5.0.11 pre-release.
• Fixes bug in AFNI install: installs shared library libnlopt-dev.

Breaking changes:

• Removes python_version option for Miniconda. Instead, specify python version in conda_install.

Changes:

• Adds support for MINC and PETPVC (thanks to @sulantha2006).
• Adds Dockerfile instructions ARG, LABEL, and VOLUME.
• Adds convenience option --run-bash.
• Adds bc/dc as dependency for FSL.
• Renames neurodocker/dockerfile.py to neurodocker/generate.py.
• Miscellaneous fixes.

At this point, the Neurodocker latest Docker image will be removed. Users will be asked to use specific versions of Neurodocker. An image with the latest master branch will also be available (tagged as master).

• neurodocker generate respects order of arguments when generating Dockerfile.
• Default entrypoint bash script is used (/neurodocker/startup.sh), and packages shell files are sourced there. This eliminates the need for some ENV layers.
• Add options --user, --install, --env, --expose. Options can be used multiple times.
• Use git describe for neurodocker version.
• Test software packages as non-root user.
• Update testing to only build Docker image if the Dockerfile has changed.
• Fix whiteout file issue in Miniconda installation.
• Add perl to FreeSurfer dependencies.
• Add cli command neurodocker reprozip-merge to merge multiple ReproZip pack files.
• Updated tests to cover additions.