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HCPprocessPipelines.def
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HCPprocessPipelines.def
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Bootstrap: docker
From: centos:7.6.1810
%help
CentOS 7.6.1810 Singularity container for StructuralPreprocessing & FunctionalPreprocessing pipelines
%labels
Version v1.1
Maintainer Connectome Coordination Facility
%post
yum install -y wget tar gzip unzip git which bzip2 bc hostname tcsh libgomp libGLU libXmu gcc qt5-qtbase libXrender xorg-x11-fonts-Type1 mesa-dri-drivers mesa-libGL-devel
mkdir -p /pipeline_tools/HCPpipelinesRunUtils
mkdir -p /NRG-data/NRG/intradb/archive
mkdir -p /NRG-data/NRG/hcpdb/archive
mkdir -p /NRG-data/NRG/hcpdb/build_ssd
########## Need gradient_coefficient_files!!! && freesurfer license key file from https://surfer.nmr.mgh.harvard.edu/fswiki/License
mkdir -p /export/HCP/gradient_coefficient_files
mkdir -p /export/freesurfer_license
cd /pipeline_tools
#### hcp_pipelines_run_utils v1.4.1
wget https://github.com/Washington-University/HCPpipelinesRunUtils/archive/v1.4.1.tar.gz -O hcp_pipelines_run_utils.tar.gz
tar xvf hcp_pipelines_run_utils.tar.gz -C /pipeline_tools/HCPpipelinesRunUtils --strip-components=1
rm hcp_pipelines_run_utils.tar.gz
#### miniconda
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /pipeline_tools/miniconda.sh
bash /pipeline_tools/miniconda.sh -b -p /opt/miniconda
rm /pipeline_tools/miniconda.sh
export PATH=/opt/miniconda/bin:${PATH}
conda create -y --name singlepython3 python=3
source activate singlepython3
conda install -y pyqt
#### install freesurfer-6.0
wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
mkdir -p /export/freesurfer-6.0
tar -C /export/freesurfer-6.0 -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz --strip-components=1 \
--exclude='freesurfer/trctrain' \
--exclude='freesurfer/average/SVIP*' \
--exclude='freesurfer/average/*/*' \
--exclude='freesurfer/lib/qt' \
--exclude='freesurfer/subjects/bert' \
--exclude='freesurfer/subjects/cvs_avg35*' \
--exclude='freesurfer/subjects/sample-00*' \
--exclude='freesurfer/subjects/fsaverage?' \
--exclude='freesurfer/subjects/fsaverage_sym' \
--exclude='freesurfer/docs/*/*' \
--exclude='freesurfer/fsfast/docs/*' \
--exclude='freesurfer/mni/mni.srcbuild.June2015.tgz'
rm freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
#### install epd-7.3.2
wget https://www.clear.rice.edu/comp140/downloads/epd/linux/epd-7.3-2-rh5-x86_64.sh
mkdir -p /export/HCP/epd-7.3.2
bash epd-7.3-2-rh5-x86_64.sh -b -p /export/HCP/epd-7.3.2
rm epd-7.3-2-rh5-x86_64.sh
rm -rf /export/HCP/epd-7.3.2/Examples/*
rm -rf /export/HCP/epd-7.3.2/Doc/*
export PATH=/export/HCP/epd-7.3.2/bin:${PATH}
yum install -y epel-release
yum install -y python2-pip.noarch openblas-devel
pip2 install numpy==1.16.2
pip2 install nibabel==2.3.0 --install-option="--prefix=/export/HCP/epd-7.3.2"
yum clean packages
rm -rf /var/cache/yum/*
#### gradunwarp v1.1.0
wget https://github.com/Washington-University/gradunwarp/archive/v1.1.0.tar.gz -O gradunwarp.tar.gz
tar -xzvf gradunwarp.tar.gz
cd gradunwarp-1.1.0/
python setup.py install --prefix=/export/HCP/epd-7.3.2
cd /pipeline_tools
rm -r gradunwarp-1.1.0
rm gradunwarp.tar.gz
#### install fsl-6.0.1
wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.1-centos7_64.tar.gz
mkdir /export/fsl-6.0.1
tar -xvzf fsl-6.0.1-centos7_64.tar.gz -C /export/fsl-6.0.1 --strip-components=1
bash /export/fsl-6.0.1/etc/fslconf/post_install.sh -f /export/fsl-6.0.1
rm fsl-6.0.1-centos7_64.tar.gz
shopt -s extglob
rm -rf /export/fsl-6.0.1/data/!(standard)
rm -rf /export/fsl-6.0.1/doc/*
rm -rf /export/fsl-6.0.1/fslpython/pkgs/*.tar.bz2
rm -rf /export/fsl-6.0.1/src/*
rm -rf /export/fsl-6.0.1/extras/src/*
#### MSM_HOCR_v3 (tagged as Release "1.0" in the GitHub repo)
wget https://github.com/ecr05/MSM_HOCR/releases/download/1.0/msm_centos
mkdir -p /export/HCP/MSM_HOCR_v3/Centos
mv msm_centos /export/HCP/MSM_HOCR_v3/Centos/msm
chmod 755 /export/HCP/MSM_HOCR_v3/Centos/msm
#### install MCR/R2012b/v80
wget http://ssd.mathworks.com/supportfiles/MCR_Runtime/R2012b/MCR_R2012b_glnxa64_installer.zip
mkdir -p /export/matlab/MCR/R2012b/M
unzip MCR_R2012b_glnxa64_installer.zip -d /export/matlab/MCR/R2012b/M
/export/matlab/MCR/R2012b/M/install -mode silent -agreeToLicense yes -destinationFolder /export/matlab/MCR/R2012b
rm -rf /export/matlab/MCR/R2012b/M
rm MCR_R2012b_glnxa64_installer.zip
ln -s /export/matlab/MCR/R2012b/v80 /export/freesurfer-6.0/MCRv80
#### install workbench
wget https://ftp.humanconnectome.org/workbench/workbench-rh_linux64-v1.3.2.zip
unzip workbench-rh_linux64-v1.3.2.zip -d /export/HCP/
rm workbench-rh_linux64-v1.3.2.zip
rm -f /export/HCP/workbench/plugins_rh_linux64/plugins.zip
#### HCPpipelines v4.0.1
wget https://github.com/Washington-University/HCPpipelines/archive/v4.0.1.tar.gz -O hcp_pipelines.tar.gz
mkdir -p /export/HCP/HCPpipelines
tar xvf hcp_pipelines.tar.gz -C /export/HCP/HCPpipelines --strip-components=1
rm hcp_pipelines.tar.gz
ln -s /export/HCP/gradient_coefficient_files/coeff_SC72C_Skyra.grad /export/HCP/HCPpipelines/global/config/coeff_SC72C_Skyra.grad
ln -s /export/HCP/gradient_coefficient_files/trunc.CMRR_7TAS_coeff_SC72CD.grad /export/HCP/HCPpipelines/global/config/trunc.CMRR_7TAS_coeff_SC72CD.grad
ln -s /export/HCP/gradient_coefficient_files/Prisma_3T_coeff_AS82.grad /export/HCP/HCPpipelines/global/config/Prisma_3T_coeff_AS82.grad
ln -s /export/freesurfer_license/license.txt /export/freesurfer-6.0/license.txt
%environment
export PATH=/opt/miniconda/bin:${PATH}
source activate singlepython3
export QT_XKB_CONFIG_ROOT=/usr/share/X11/xkb
export HCP_RUN_UTILS=/pipeline_tools/HCPpipelinesRunUtils
export FSLDIR=/export/fsl-6.0.1
source ${FSLDIR}/etc/fslconf/fsl.sh
export FSL_DIR="${FSLDIR}"
export FREESURFER_HOME=/export/freesurfer-6.0
source ${FREESURFER_HOME}/SetUpFreeSurfer.sh
export EPD_PYTHON_HOME=/export/HCP/epd-7.3.2
export PATH=${EPD_PYTHON_HOME}/bin:${PATH}
export CARET7DIR=/export/HCP/workbench/bin_rh_linux64
export HCPPIPEDIR=/export/HCP/HCPpipelines
export HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config
export HCPPIPEDIR_Global=${HCPPIPEDIR}/global/scripts
export HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates
export HCPPIPEDIR_PreFS=${HCPPIPEDIR}/PreFreeSurfer/scripts
export HCPPIPEDIR_FS=${HCPPIPEDIR}/FreeSurfer/scripts
export HCPPIPEDIR_PostFS=${HCPPIPEDIR}/PostFreeSurfer/scripts
export HCPPIPEDIR_fMRISurf=${HCPPIPEDIR}/fMRISurface/scripts
export HCPPIPEDIR_fMRIVol=${HCPPIPEDIR}/fMRIVolume/scripts
export HCPPIPEDIR_dMRI=${HCPPIPEDIR}/DiffusionPreprocessing/scripts
export HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts
export MSMBINDIR=/export/HCP/MSM_HOCR_v3/Centos
export MSMCONFIGDIR=${HCPPIPEDIR}/MSMConfig
export PYTHONPATH=${HCP_RUN_UTILS}/lib
export PATH=${HCPPIPEDIR}/FreeSurfer/custom:${PATH}