Skip to content

Commit 70f3ef5

Browse files
author
Jakub Kaczmarzyk
authored
Merge pull request #244 from kaczmarj/maint/0.4.3
update to version 0.4.3
2 parents 18c7a8b + 0b11009 commit 70f3ef5

File tree

2 files changed

+67
-75
lines changed

2 files changed

+67
-75
lines changed

‎README.md‎

Lines changed: 66 additions & 74 deletions
Original file line numberDiff line numberDiff line change
@@ -15,13 +15,12 @@ _Neurodocker_ is a command-line program that generates custom Dockerfiles and Si
1515
- [Example of minimizing Docker image for FreeSurfer recon-all](https://github.com/freesurfer/freesurfer/issues/70#issuecomment-316361886)
1616
- [Known issues](#known-issues)
1717

18-
1918
# Installation
2019

2120
Use the _Neurodocker_ Docker image (recommended):
2221

2322
```shell
24-
$ docker run --rm kaczmarj/neurodocker:0.4.2 --help
23+
$ docker run --rm kaczmarj/neurodocker:0.4.3 --help
2524
```
2625

2726
_Note_: Do not use the `-t/--tty` flag with `docker run` or non-printable characters will be a part of the output (see [moby/moby#8513 (comment)](https://github.com/moby/moby/issues/8513#issuecomment-216191236)).
@@ -41,73 +40,70 @@ $ pip install --user neurodocker
4140

4241
Note: it is not yet possible to minimize Docker containers using the _Neurodocker_ Docker image.
4342

44-
4543
# Supported software
4644

47-
| software | argument | description |
48-
| -------- | -------- | ----------- |
49-
| **AFNI** | version* | latest |
50-
| | method | binaries (default), source. Install pre-compiled binaries or build form source. |
51-
| | install_path | Installation path. Default `/opt/afni-{version}`. |
52-
| | install_r | If true, install R. |
53-
| | install_r_pkgs | If true, install R and AFNI's R packages. |
54-
| | install_python2 | If true, install Python 2. |
55-
| | install_python3 | If true, install Python 3. |
56-
| **ANTs** | version* | 2.3.1, 2.3.0, 2.2.0, 2.1.0, 2.0.3, or 2.0.0. If `method=source`, version can be a git commit hash or branch. |
57-
| | method | binaries (default), source. |
58-
| | install_path | Installation path. Default `/opt/ants-{version}`. |
59-
| | cmake_opts | If `method=source`, options for `cmake`. |
60-
| | make_opts | If `method=source`, options for `make`. |
61-
| **Convert3D** | version* | 1.0.0 or nightly. |
62-
| | method | binaries (default) |
63-
| | install_path | Installation path. Default `/opt/convert3d-{version}`. |
64-
| **dcm2niix** | version* | latest, git commit hash or branch. |
65-
| | method | source (default) |
66-
| | install_path | Installation path. Default `/opt/dcm2niix-{version}`. |
67-
| | cmake_opts | If `method=source`, options for `cmake`. |
68-
| | make_opts | If `method=source`, options for `make`. |
69-
| **FreeSurfer** | version* | 6.0.0-min |
70-
| | method | binaries (default) |
71-
| | install_path | Installation path. Default `/opt/freesurfer-{version}`. |
72-
| | exclude_paths | Sequence of space-separated path(s) to exclude when inflating the tarball. |
73-
| | license_path | Relative path to license file. If provided, this file will be copied into the Docker image. Must be within the build context. |
74-
| **FSL**** | version* | 5.0.11, 5.0.10, 5.0.9, 5.0.8 |
75-
| | method | binaries (default) |
76-
| | install_path | Installation path. Default `/opt/fsl-{version}`. |
77-
| | exclude_paths | Sequence of space-separated path(s) to exclude when inflating the tarball. |
78-
| **Matlab Compiler Runtime** | version* | 2018a, 2012-17[a-b], 2010a |
79-
| | method | binaries (default) |
80-
| | install_path | Installation path. Default `/opt/matlabmcr-{version}`. |
81-
| **MINC** | version* | 1.9.15 |
82-
| | method | binaries (default) |
83-
| | install_path | Installation path. Default `/opt/minc-{version}`. |
84-
| **Miniconda** | version | latest (default), all other hosted versions. |
85-
| | install_path | Installation path. Default `/opt/miniconda-{version}`. |
86-
| | create_env | Name of conda environment to create. |
87-
| | use_env | Name of previously installed environment. |
88-
| | conda_install | Packages to install with `conda`. E.g., `conda_install="python=3.6 numpy traits"` |
89-
| | pip_install | Packages to install with `pip`. |
90-
| | activate | If true (default), activate this environment in container entrypoint. |
91-
| **MRtrix3** | version* | 3.0 |
92-
| | method | binaries (default) |
93-
| | install_path | Installation path. Default `/opt/mrtrix3-{version}`. |
94-
| **NeuroDebian** | os_codename* | Codename of the operating system (e.g., stretch, zesty). |
95-
| | server* | Server to download NeuroDebian packages from. Choose the one closest to you. See `neurodocker generate docker --help` for the full list of servers. |
96-
| | full | If true (default), use non-free sources. If false, use libre sources. |
97-
| **PETPVC** | version* | 1.2.2, 1.2.1, 1.2.0-b, 1.2.0-a, 1.1.0, 1.0.0 |
98-
| | method | binaries (default) |
99-
| | install_path | Installation path. Default `/opt/petpvc-{version}`. |
100-
| **SPM12** | version* | r7219, r6914, r6685, r6472, r6225 |
101-
| | install_path | Installation path. Default `/opt/spm12-{version}`. |
102-
| | | _Note: Matlab Compiler Runtime is installed when SPM12 is installed._ |
103-
| **VNC** | passwd* | Choose a password for this VNC server. |
104-
| | start_at_runtime | If true, start the VNC server at container runtime. False by default. |
105-
| | geometry | The geometry of the VNC session (e.g., `1920x1080`). |
106-
107-
108-
\* required argument.
109-
** FSL is non-free. If you are considering commercial use of FSL, please consult the [relevant license](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence).
110-
45+
| software | argument | description |
46+
| --------------------------- | ---------------- | --------------------------------------------------------------------------------------------------------------------------------------------------- |
47+
| **AFNI** | version\* | latest |
48+
| | method | binaries (default), source. Install pre-compiled binaries or build form source. |
49+
| | install_path | Installation path. Default `/opt/afni-{version}`. |
50+
| | install_r | If true, install R. |
51+
| | install_r_pkgs | If true, install R and AFNI's R packages. |
52+
| | install_python2 | If true, install Python 2. |
53+
| | install_python3 | If true, install Python 3. |
54+
| **ANTs** | version\* | 2.3.1, 2.3.0, 2.2.0, 2.1.0, 2.0.3, or 2.0.0. If `method=source`, version can be a git commit hash or branch. |
55+
| | method | binaries (default), source. |
56+
| | install_path | Installation path. Default `/opt/ants-{version}`. |
57+
| | cmake_opts | If `method=source`, options for `cmake`. |
58+
| | make_opts | If `method=source`, options for `make`. |
59+
| **Convert3D** | version\* | 1.0.0 or nightly. |
60+
| | method | binaries (default) |
61+
| | install_path | Installation path. Default `/opt/convert3d-{version}`. |
62+
| **dcm2niix** | version\* | latest, git commit hash or branch. |
63+
| | method | source (default) |
64+
| | install_path | Installation path. Default `/opt/dcm2niix-{version}`. |
65+
| | cmake_opts | If `method=source`, options for `cmake`. |
66+
| | make_opts | If `method=source`, options for `make`. |
67+
| **FreeSurfer** | version\* | 6.0.0-min |
68+
| | method | binaries (default) |
69+
| | install_path | Installation path. Default `/opt/freesurfer-{version}`. |
70+
| | exclude_paths | Sequence of space-separated path(s) to exclude when inflating the tarball. |
71+
| | license_path | Relative path to license file. If provided, this file will be copied into the Docker image. Must be within the build context. |
72+
| **FSL\*\*** | version\* | 5.0.11, 5.0.10, 5.0.9, 5.0.8 |
73+
| | method | binaries (default) |
74+
| | install_path | Installation path. Default `/opt/fsl-{version}`. |
75+
| | exclude_paths | Sequence of space-separated path(s) to exclude when inflating the tarball. |
76+
| **Matlab Compiler Runtime** | version\* | 2018a, 2012-17[a-b], 2010a |
77+
| | method | binaries (default) |
78+
| | install_path | Installation path. Default `/opt/matlabmcr-{version}`. |
79+
| **MINC** | version\* | 1.9.15 |
80+
| | method | binaries (default) |
81+
| | install_path | Installation path. Default `/opt/minc-{version}`. |
82+
| **Miniconda** | version | latest (default), all other hosted versions. |
83+
| | install_path | Installation path. Default `/opt/miniconda-{version}`. |
84+
| | create_env | Name of conda environment to create. |
85+
| | use_env | Name of previously installed environment. |
86+
| | conda_install | Packages to install with `conda`. E.g., `conda_install="python=3.6 numpy traits"` |
87+
| | pip_install | Packages to install with `pip`. |
88+
| | activate | If true (default), activate this environment in container entrypoint. |
89+
| **MRtrix3** | version\* | 3.0 |
90+
| | method | binaries (default) |
91+
| | install_path | Installation path. Default `/opt/mrtrix3-{version}`. |
92+
| **NeuroDebian** | os_codename\* | Codename of the operating system (e.g., stretch, zesty). |
93+
| | server\* | Server to download NeuroDebian packages from. Choose the one closest to you. See `neurodocker generate docker --help` for the full list of servers. |
94+
| | full | If true (default), use non-free sources. If false, use libre sources. |
95+
| **PETPVC** | version\* | 1.2.2, 1.2.1, 1.2.0-b, 1.2.0-a, 1.1.0, 1.0.0 |
96+
| | method | binaries (default) |
97+
| | install_path | Installation path. Default `/opt/petpvc-{version}`. |
98+
| **SPM12** | version\* | r7219, r6914, r6685, r6472, r6225 |
99+
| | install_path | Installation path. Default `/opt/spm12-{version}`. |
100+
| | | _Note: Matlab Compiler Runtime is installed when SPM12 is installed._ |
101+
| **VNC** | passwd\* | Choose a password for this VNC server. |
102+
| | start_at_runtime | If true, start the VNC server at container runtime. False by default. |
103+
| | geometry | The geometry of the VNC session (e.g., `1920x1080`). |
104+
105+
\* required argument.
106+
\*\* FSL is non-free. If you are considering commercial use of FSL, please consult the [relevant license](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence).
111107

112108
# Generate Dockerfile
113109

@@ -235,15 +231,14 @@ The canonical examples install ANTs version 2.3.1 on Debian 9 (Stretch).
235231

236232
_Note_: Do not use the `-t/--tty` flag with `docker run` or non-printable characters will be a part of the output (see [moby/moby#8513 (comment)](https://github.com/moby/moby/issues/8513#issuecomment-216191236)).
237233

238-
239234
### Docker
240235

241236
```shell
242-
$ docker run --rm kaczmarj/neurodocker:0.4.2 generate docker \
237+
$ docker run --rm kaczmarj/neurodocker:0.4.3 generate docker \
243238
--base debian:stretch --pkg-manager apt --ants version=2.3.1
244239

245240
# Build image by piping Dockerfile to `docker build`
246-
$ docker run --rm kaczmarj/neurodocker:0.4.2 generate docker \
241+
$ docker run --rm kaczmarj/neurodocker:0.4.3 generate docker \
247242
--base debian:stretch --pkg-manager apt --ants version=2.3.1 | docker build -
248243
```
249244

@@ -252,18 +247,16 @@ $ docker run --rm kaczmarj/neurodocker:0.4.2 generate docker \
252247
Install ANTs on Debian 9 (Stretch).
253248

254249
```shell
255-
$ docker run --rm kaczmarj/neurodocker:0.4.2 generate singularity \
250+
$ docker run --rm kaczmarj/neurodocker:0.4.3 generate singularity \
256251
--base debian:stretch --pkg-manager apt --ants version=2.3.1
257252
```
258253

259-
260254
## Minimize existing Docker image
261255

262256
_Neurodocker_ must be `pip` installed for container minimization.
263257

264258
In the following example, a Docker image is built with ANTs version 2.3.1 and a functional scan. The image is minified for running `antsMotionCorr`. The original ANTs Docker image is 1.85 GB, and the "minified" image is 365 MB.
265259

266-
267260
```shell
268261
# Create a Docker image with ANTs, and download a functional scan.
269262
$ download_cmd="curl -sSL -o /home/func.nii.gz http://psydata.ovgu.de/studyforrest/phase2/sub-01/ses-movie/func/sub-01_ses-movie_task-movie_run-1_bold.nii.gz"
@@ -282,7 +275,6 @@ $ neurodocker reprozip trace ants-container "$cmd"
282275
$ reprounzip docker setup neurodocker-reprozip.rpz test
283276
```
284277

285-
286278
# Known issues
287279

288280
- Using the `-t/--tty` option in `docker run` produces non-printable characters in the generated Dockerfile or Singularity recipe (see [moby/moby#8513 (comment)](https://github.com/moby/moby/issues/8513#issuecomment-216191236)).

‎neurodocker/version.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
Copied from https://github.com/nipy/nipype/blob/master/nipype/info.py.
44
"""
55

6-
__version__ = '0.4.3-dev'
6+
__version__ = '0.4.3'
77

88

99
def get_gitversion():

0 commit comments

Comments
 (0)