ADD: mricron (#300)

* add mricron pre-compiled * add latest compiled version * add examples for mricron
ReproNim · Oct 3, 2019 · f49345e · f49345e
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diff --git a/README.md b/README.md
@@ -85,6 +85,8 @@ Note: it is not yet possible to minimize Docker containers using the _Neurodocke
 |                             | conda_install    | Packages to install with `conda`. E.g., `conda_install="python=3.6 numpy traits"`                                                                   |
 |                             | pip_install      | Packages to install with `pip`.                                                                                                                     |
 |                             | activate         | If true (default), activate this environment in container entrypoint.                                                                               |
+| **MRIcron** | version\* | latest, 1.0.20190902, 1.0.20190410, 1.0.20181114, 1.0.20180614, 1.0.20180404, 1.0.20171220 |
+| | install_path | Installation path. Default `/opt/mricron-{version}` |
 | **MRtrix3**                 | version\*        | 3.0                                                                                                                                                 |
 |                             | method           | binaries (default)                                                                                                                                  |
 |                             | install_path     | Installation path. Default `/opt/mrtrix3-{version}`.                                                                                                |

diff --git a/examples/README.md b/examples/README.md
@@ -30,6 +30,7 @@ All of the examples below use `debian:stretch` as the base image, but any Docker
   - [Matlab Compiler Runtime (MCR)](#matlab-compiler-runtime-mcr)
   - [MINC](#minc)
   - [Miniconda](#miniconda)
+  - [MRIcron](#mricron)
   - [MRtrix3](#mrtrix3)
   - [NeuroDebian](#neurodebian)
   - [PETPVC](#petpvc)
@@ -318,6 +319,13 @@ neurodocker generate [docker|singularity] --base=debian:stretch --pkg-manager=ap
               yaml_file=/opt/environment.yml
 ```
 
+## MRIcron
+
+```shell
+neurodocker generate [docker|singularity] --base=debian:stretch --pkg-manager=apt \
+  --mricron version=latest
+```
+
 ## MRtrix3
 
 ```shell

diff --git a/neurodocker/interfaces/interfaces.py b/neurodocker/interfaces/interfaces.py
@@ -249,6 +249,16 @@ def render_env(self):
             return super().render_env()
 
 
+class MINC(_BaseInterface):
+    """Create instance of MRIcron object."""
+
+    _name = 'mricron'
+    _pretty_name = 'MRIcron'
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(self._name, *args, **kwargs)
+
+
 class MRtrix3(_BaseInterface):
     """Create instance of MRtrix3 object."""
 

diff --git a/neurodocker/neurodocker.py b/neurodocker/neurodocker.py
@@ -161,6 +161,9 @@ def _add_generate_common_arguments(parser):
         " (defaults to latest). The options conda_install and"
         " pip_install accept strings of packages: conda_install="
         '"python=3.6 numpy traits".',
+        "mricron":
+        "Install MRIcron. valid keys are version (required), method, and"
+        " install_path.",
         "mrtrix3":
         "Install MRtrix3. Valid keys are version (required),"
         " method, and install_path",

diff --git a/neurodocker/templates/mricron.yaml b/neurodocker/templates/mricron.yaml
@@ -0,0 +1,28 @@
+# Instructions to install MRIcron.
+#
+# Repository: https://github.com/neurolabusc/MRIcron
+
+generic:
+  binaries:
+    urls:
+      latest: https://github.com/neurolabusc/MRIcron/releases/latest/download/MRIcron_linux.zip
+      "1.0.20190902": https://github.com/neurolabusc/MRIcron/releases/download/v1.0.20190902/MRIcron_linux.zip
+      "1.0.20190410": https://github.com/neurolabusc/MRIcron/releases/download/v1.0.20190410/mricron_linux.zip
+      "1.0.20181114": https://github.com/neurolabusc/MRIcron/releases/download/v1.0.20181114/mricron_linux.zip
+      "1.0.20180614": https://github.com/neurolabusc/MRIcron/releases/download/v1.0.20180614/mricron_linux.zip
+      "1.0.20180404": https://github.com/neurolabusc/MRIcron/releases/download/v1.0.20180404/mricron_lx64.zip
+      "1.0.20171220": https://github.com/neurolabusc/MRIcron/releases/download/v1.0.20171220/mricron_linux.zip
+    dependencies:
+      apt: libgtk2.0-0
+      yum: gtk2
+    env:
+      PATH: "{{ mricron.install_path }}:$PATH"
+    instructions: |
+      {{ mricron.install_dependencies() }}
+      echo "Downloading MRIcron ..."
+      mkdir -p {{ mricron.install_path }}
+      curl {{ mricron.curl_opts }} -O {{ mricron.binaries_url }}
+      unzip "*cron*.zip"
+      rm -f "*cron*.zip"
+      mv mricron/* {{ mricron.install_path }}
+      rmdir mricron