...
 
Commits (8)
......@@ -4,9 +4,7 @@ variables:
build:
stage: build
tags:
- docker
script:
- sudo docker build -t $repo/$tag .
- sudo docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $repo
- sudo docker push $repo/$tag
- docker build -t $repo/$tag .
- docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $repo
- docker push $repo/$tag
# To build this image, you'll need to download FreeSurfer, MNE, DCMTK
# and have a valid FreeSurfer license file.
FROM ubuntu:16.04
FROM gitlab.thevirtualbrain.org:5000/docker/ubuntu
MAINTAINER Marmaduke Woodman <marmaduke.woodman@univ-amu.fr>
WORKDIR /opt
......@@ -62,3 +62,13 @@ RUN git clone https://github.com/mrtrix3/mrtrix3 && cd mrtrix3 \
&& git checkout 0.3.16 && ./configure -nogui && ./build
ENV MRT3=/opt/mrtrix3
ENV PATH=$MRT3/release/bin:$MRT3/scripts:$PATH
# setup Python stack
RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
RUN bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda
ENV PATH=/opt/conda/bin:$PATH
ADD conda.yml /opt/conda-env.yml
RUN pip install numpy matplotlib scipy ipykernel scikit-learn mne numba numexpr pandas xlrd networkx nibabel nilearn
RUN pip install cython && pip install gdist
# conda env create -f /opt/conda-env.yml
name: pipeline
channels:
- https://repo.continuum.io/pkgs/free
- defaults
dependencies:
- _libgcc_mutex=0.1=main
- blas=1.0=openblas
- cycler=0.10.0=py36_0
- cython=0.25.2=py36_0
- dbus=1.10.10=0
- decorator=4.1.2=py36_0
- expat=2.1.0=0
- fontconfig=2.12.1=3
- freetype=2.5.5=2
- glib=2.50.2=1
- gst-plugins-base=1.8.0=0
- gstreamer=1.8.0=0
- icu=54.1=0
- ipykernel=4.6.1=py36_0
- ipython=6.1.0=py36_0
- ipython_genutils=0.2.0=py36_0
- jedi=0.10.2=py36_2
- jpeg=9b=0
- jupyter_client=5.1.0=py36_0
- jupyter_core=4.3.0=py36_0
- libffi=3.2.1=1
- libgcc=7.2.0=h69d50b8_2
- libgcc-ng=9.1.0=hdf63c60_0
- libgfortran=3.0.0=1
- libiconv=1.14=0
- libpng=1.6.27=0
- libsodium=1.0.10=0
- libstdcxx-ng=7.2.0=h7a57d05_2
- libxcb=1.12=1
- libxml2=2.9.4=0
- llvmlite=0.18.0=py36_0
- matplotlib=2.0.2=np112py36_0
- nomkl=1.0=0
- numba=0.33.0=np112py36_0
- numexpr=2.6.2=np112py36_nomkl_0
- numpy=1.12.1=py36_nomkl_0
- openblas=0.2.19=0
- openssl=1.0.2l=0
- pandas=0.22.0=py36hf484d3e_0
- path.py=10.3.1=py36_0
- pcre=8.39=1
- pexpect=4.2.1=py36_0
- pickleshare=0.7.4=py36_0
- pip=9.0.1=py36_1
- prompt_toolkit=1.0.15=py36_0
- ptyprocess=0.5.2=py36_0
- pygments=2.2.0=py36_0
- pyparsing=2.1.4=py36_0
- pyqt=5.6.0=py36_2
- python=3.6.1=2
- python-dateutil=2.6.0=py36_0
- pytz=2017.2=py36_0
- pyzmq=16.0.2=py36_0
- qt=5.6.2=4
- readline=6.2=2
- scikit-learn=0.18.1=np112py36_nomkl_1
- scipy=0.19.0=np112py36_nomkl_0
- setuptools=27.2.0=py36_0
- simplegeneric=0.8.1=py36_1
- sip=4.18=py36_0
- six=1.10.0=py36_0
- sqlite=3.13.0=0
- tk=8.5.18=0
- tornado=4.5.2=py36_0
- traitlets=4.3.2=py36_0
- wcwidth=0.1.7=py36_0
- wheel=0.29.0=py36_0
- xlrd=1.1.0=py36h1db9f0c_1
- xz=5.2.2=1
- zeromq=4.1.5=0
- zlib=1.2.8=3
- pip:
- gdist==1.0.3
- mako==1.0.6
- markupsafe==1.0
- mne==0.15.2
- networkx==1.11
- nibabel==2.4.0
- nilearn==0.3.0
- psutil==5.2.2
- pystan==2.15.0.1
- salib==1.0.3
- seaborn==0.7.1
prefix: /opt/python-stack