diff --git a/.circleci/config.yml b/.circleci/config.yml index a14babc5..4b1819d6 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -23,6 +23,7 @@ jobs: steps: - attach_workspace: at: /tmp/workspace + - checkout - run: docker load -i /tmp/workspace/docker/image.tar - run: name: push to dockerhub diff --git a/INSTALL.md b/INSTALL.md index daa056cf..a0b7dbd3 100644 --- a/INSTALL.md +++ b/INSTALL.md @@ -52,7 +52,7 @@ docker images The Dockerfile used to create the image stored on DockerHub is available at the root of the repository ([Dockerfile](Dockerfile)). But you might want to personalize this Dockerfile. To do so, change the command below that will generate a new Dockerfile: ```bash - docker run --rm repronim/neurodocker:0.9.5 generate docker \ + neurodocker generate docker \ --base-image centos:7 --pkg-manager yum \ --yes \ --install git \ @@ -61,8 +61,9 @@ The Dockerfile used to create the image stored on DockerHub is available at the --spm12 version=r7771 method=binaries \ --miniconda method=binaries \ version=latest \ + mamba=true \ conda_install="python=3.10 pip=23.2.1" \ - pip_install="traits==6.3.0 jupyterlab-4.0.6 graphviz-0.20.1 nipype==1.8.6 scikit-image==0.21.0 matplotlib==3.8.0 nilearn==0.10.1" \ + pip_install="traits==6.3.0 jupyterlab==4.0.6 graphviz==0.20.1 nipype==1.8.6 scikit-image==0.21.0 matplotlib==3.8.0 nilearn==0.10.1" \ --run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' > Dockerfile ``` diff --git a/makefile b/makefile index 26347dd9..c73c7ac7 100644 --- a/makefile +++ b/makefile @@ -1,20 +1,10 @@ .PHONY: Dockerfile -Dockerfile: - docker run --rm repronim/neurodocker:0.9.5 generate docker \ - --base-image centos:7 --pkg-manager yum \ - --yes \ - --install git \ - --ants method=binaries version=2.4.3 \ - --fsl version=6.0.6.4 \ - --spm12 version=r7771 method=binaries \ - --miniconda method=binaries \ - version=latest - conda_install="python=3.10 pip=23.2.1" \ - pip_install="traits==6.3.0 jupyterlab==4.0.6 graphviz==0.20.1 nipype==1.8.6 scikit-image==0.21.0 matplotlib==3.8.0 nilearn==0.10.1" \ - --run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' > Dockerfile +# docker run --rm repronim/neurodocker:0.9.5 generate docker -Dockerfile_mamba: +# using the mamba option requires to use the version of neurodocker +# installed from the main branch of the the neurodocker github repo +Dockerfile: neurodocker generate docker \ --base-image centos:7 --pkg-manager yum \ --yes \