Update build.sh

recipes/micapipe/build.sh

@@ -7,7 +7,7 @@
 set -e
 
 export toolName='micapipe'
-export toolVersion='0.1.2'
+export toolVersion='v0.1.2'
 # Don't forget to update version change in README.md!!!!!
 
 if [ "$1" != "" ]; then
@@ -18,54 +18,16 @@ fi
 source ../main_setup.sh
 
 # Generate Dockerfile.
-neurodocker generate ${neurodocker_buildMode}
-    --base=ubuntu:bionic-20201119 \
-    --pkg-manager apt \
-    --install "gcc g++ lsb-core bsdtar jq libopenblas-dev tree openjdk-8-jdk libstdc++6" \
-    --dcm2niix version=v1.0.20190902 method=source\
-    --fsl version=6.0.0 \
-    --run-bash 'bash /opt/fsl-6.0.0/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.0' \
-    --freesurfer version=6.0.0 \
-    --matlabmcr version=2017b\
-    --afni version=latest\
-    --ants version=2.3.4 \
-    --run-bash "apt-get update && apt-get install -y gnupg2 && wget -O- http://neuro.debian.net/lists/xenial.de-fzj.full | tee /etc/apt/sources.list.d/neurodebian.sources.list && apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9 && apt-get update && apt-get install -y connectome-workbench=1.3.2-2~nd16.04+1" \
-    --run-bash "cd /opt/ && wget http://www.fmrib.ox.ac.uk/~steve/ftp/fix1.068.tar.gz && tar xvfz fix1.068.tar.gz && rm fix1.068.tar.gz" \
-    --user=mica \
-    --miniconda \
-      conda_install="python=3.7 certifi==2020.6.20
-                     cycler==0.10.0 joblib==0.16.0
-                     kiwisolver==1.2.0 matplotlib==3.3.1 nibabel==3.1.1
-                     numpy==1.19.1 packaging==20.4 pandas==1.1.1 nilearn
-                     pillow==7.2.0 pyparsing==2.4.7 python-dateutil==2.8.1
-                     pytz==2020.1 scikit-learn==0.23.2 scipy==1.5.2
-                     six==1.15.0 threadpoolctl==2.1.0 vtk==9.0.1"\
-      pip_install='brainspace==0.1.1 argparse==1.1' \
-      create_env="micapipe" \
-      activate=true \
-    --run-bash 'source activate micapipe && conda install -c mrtrix3 mrtrix3==3.0.1 && pip install git+https://github.com/MICA-MNI/ENIGMA.git' \
-    --user=root\
-    --run "set -uex; \
-           LD_LIBRARY_PATH=/lib64/:$PATH; \
-           apt install -y software-properties-common apt-transport-https; \
-           apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9; \
-           add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'; \
-           apt update; \
-           apt install -y r-base libblas-dev liblapack-dev gfortran g++ libgl1-mesa-glx; \
-           rm -rf /var/lib/apt/lists/*;" \
-    --run-bash "wget https://www.dropbox.com/s/47lu1nojrderls1/install_R_env.sh?dl=0 -O /opt/install_R_env.sh && 
-                bash /opt/install_R_env.sh && cd /opt/afni-latest && rPkgsInstall -pkgs ALL" \
-    --copy . /opt/micapipe \
-    --run-bash "cd /opt/micapipe && mv fix_settings.sh /opt/fix1.068/settings.sh && mv fsl_conf/* /opt/fsl-6.0.0/etc/flirtsch/" \
-    --run-bash "mv /opt/micapipe/surfaces/fsaverage5 /opt/freesurfer-6.0.0/subjects" \
-    --workdir='/home/mica' \
-    --env MICAPIPE='/opt/micapipe'\
-    --add-to-entrypoint "source /opt/freesurfer-6.0.0/SetUpFreeSurfer.sh" \
-    --add-to-entrypoint "export FIXPATH=/opt/fix && export PATH="${FIXPATH}:${PATH}"" \
-    --entrypoint "/neurodocker/startup.sh /opt/micapipe/mica-pipe" \
-    --copy README.md /README.md                          `# include readme file in container` \
-    --copy test.sh /test.sh                              `# include test file in container` \
-    > ${imageName}.${neurodocker_buildExt}
+neurodocker generate ${neurodocker_buildMode} \
+   --base-image micalab/${toolName}:${toolVersion} \
+   --pkg-manager apt \
+   --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \
+   --run="chmod +x /usr/bin/ll" \
+   --run="mkdir ${mountPointList}" \
+   --copy README.md /README.md \
+  > ${imageName}.${neurodocker_buildExt}
+
+
 
 if [ "$1" != "" ]; then
    ./../main_build.sh