diff --git a/recipes/deepretinotopy/build.sh b/recipes/deepretinotopy/build.sh index 673daa0e..a8c68839 100755 --- a/recipes/deepretinotopy/build.sh +++ b/recipes/deepretinotopy/build.sh @@ -18,6 +18,7 @@ neurodocker generate ${neurodocker_buildMode} \ --base-image ghcr.io/neurodesk/freesurfer_7.3.2:20230216 \ --pkg-manager yum \ --install git \ + --run="mkdir -p ${mountPointList}" \ --miniconda version=py37_4.8.3 \ conda_install='cudatoolkit=10.2' \ pip_install='packaging torch==1.6.0 torchvision==0.7.0 pandas==1.1.5 seaborn==0.11.1 nibabel==3.2.1 torch-geometric==1.6.3 scikit-learn==0.22.2 scipy==1.5.4 matplotlib==3.3.4 osfclient==0.0.5' \ diff --git a/recipes/glmsingle/build.sh b/recipes/glmsingle/build.sh index 64856a76..482c81d3 100755 --- a/recipes/glmsingle/build.sh +++ b/recipes/glmsingle/build.sh @@ -12,6 +12,7 @@ neurodocker generate ${neurodocker_buildMode} \ --base-image ubuntu:20.04 \ --pkg-manager apt \ --env DEBIAN_FRONTEND=noninteractive \ + --run="mkdir -p ${mountPointList}" \ --install python3.8 python3-pip libpython3.8-dev git \ --run 'python3.8 -m pip install git+https://github.com/cvnlab/GLMsingle.git@1.2' \ --run 'python3.8 -m pip install ipykernel jupyterlab' \ diff --git a/recipes/hnncore/build.sh b/recipes/hnncore/build.sh index e6d02f0c..4962c28f 100644 --- a/recipes/hnncore/build.sh +++ b/recipes/hnncore/build.sh @@ -14,6 +14,7 @@ neurodocker generate ${neurodocker_buildMode} \ --base-image ubuntu:22.04 \ --pkg-manager apt \ --env DEBIAN_FRONTEND=noninteractive \ + --run="mkdir -p ${mountPointList}" \ --install python3.9 python3-pip libpython3-dev build-essential openmpi-bin openmpi-doc libopenmpi-dev \ --run 'pip install numpy scipy matplotlib NEURON' \ --run 'pip install ipywidgets voila scikit-learn joblib mpi4py psutil' \ diff --git a/recipes/mrsiproc/build.sh b/recipes/mrsiproc/build.sh index a2412515..8b1ece04 100755 --- a/recipes/mrsiproc/build.sh +++ b/recipes/mrsiproc/build.sh @@ -38,6 +38,7 @@ source ../main_setup.sh neurodocker generate ${neurodocker_buildMode} \ --base-image vnmd/fsl_${fslVersion} \ --pkg-manager apt \ + --run="mkdir -p ${mountPointList}" \ --user=root `# otherwise some permission denied error occurs during docker build` \ --dcm2niix method=source version=${dcm2niixVersion} \ --minc version=${mincVersion} \ diff --git a/recipes/mrtrix3src/build.sh b/recipes/mrtrix3src/build.sh index 4a66ab99..c868b924 100755 --- a/recipes/mrtrix3src/build.sh +++ b/recipes/mrtrix3src/build.sh @@ -16,6 +16,7 @@ source ../main_setup.sh neurodocker generate ${neurodocker_buildMode} \ --base-image vnmd/fsl_6.0.5.1:20221016 \ --pkg-manager apt \ + --run="mkdir -p ${mountPointList}" \ --ants version="2.3.4" \ --workdir /opt \ --install dbus-x11 less python3-distutils mesa-common-dev libglu1-mesa qt5-default libqt5svg5-dev wget libqt5opengl5-dev libqt5opengl5 libqt5gui5 libqt5core5a libtiff5-dev libtiff5 libfftw3-dev liblapack3 libeigen3-dev \ diff --git a/recipes/mrtrix3tissue/build.sh b/recipes/mrtrix3tissue/build.sh index 498738d5..6297ceb0 100644 --- a/recipes/mrtrix3tissue/build.sh +++ b/recipes/mrtrix3tissue/build.sh @@ -19,6 +19,7 @@ fi neurodocker generate ${neurodocker_buildMode} \ --base-image ghcr.io/neurodesk/caid/fsl_6.0.3:20200905 \ --pkg-manager apt \ + --run="mkdir -p ${mountPointList}" \ --${toolName} version=master method="source" \ --ants version="2.3.4" \ --env DEPLOY_PATH=/opt/${toolName}-master/bin/ \ diff --git a/recipes/pydeface/build.sh b/recipes/pydeface/build.sh index 22b12991..23aa222e 100644 --- a/recipes/pydeface/build.sh +++ b/recipes/pydeface/build.sh @@ -15,6 +15,7 @@ neurodocker generate ${neurodocker_buildMode} \ --base-image vnmd/fsl_6.0.3:20200905 \ --pkg-manager apt \ --user root \ + --run="mkdir -p ${mountPointList}" \ --env DEBIAN_FRONTEND=noninteractive \ --install ca-certificates \ --miniconda version=latest \ diff --git a/recipes/qsmxtbase/build.sh b/recipes/qsmxtbase/build.sh index ec881e66..2dbaa258 100755 --- a/recipes/qsmxtbase/build.sh +++ b/recipes/qsmxtbase/build.sh @@ -26,6 +26,7 @@ yes | neurodocker generate ${neurodocker_buildMode} \ --env DEBIAN_FRONTEND=noninteractive \ --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \ --run="chmod +x /usr/bin/ll" \ + --run="mkdir -p ${mountPointList}" \ --install bzip2 ca-certificates wget unzip gcc cmake g++ dbus-x11 libgtk2.0-0 git graphviz wget \ zip libgl1 libglib2.0 libglu1-mesa libsm6 libxrender1 libxt6 libxcomposite1 libfreetype6 \ libasound2 libfontconfig1 libxkbcommon0 libxcursor1 libxi6 libxrandr2 libxtst6 qt5-default \