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environment logic change #1134

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merged 1 commit into from
May 31, 2024
Merged

environment logic change #1134

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21 changes: 12 additions & 9 deletions environment
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Original file line number Diff line number Diff line change
@@ -1,18 +1,21 @@
PROJECT=%PROJECT%
MINC_TOOLKIT_DIR=%MINC_TOOLKIT_DIR%

# to source the MINC toolkit
source %MINC_TOOLKIT_DIR%/minc-toolkit-config.sh
source ${MINC_TOOLKIT_DIR}/minc-toolkit-config.sh
umask 0002

# export PATH, PERL5LIB, TMPDIR and LORIS_CONFIG variables
export PATH=/opt/%PROJECT%/bin/mri:/opt/%PROJECT%/bin/mri/uploadNeuroDB:/opt/%PROJECT%/bin/mri/uploadNeuroDB/bin:/opt/%PROJECT%/bin/mri/dicom-archive:/opt/%PROJECT%/bin/mri/python:/opt/%PROJECT%/bin/mri/tools:/opt/%PROJECT%/bin/mri/python/react-series-data-viewer:%MINC_TOOLKIT_DIR%/bin:/usr/local/bin/tpcclib:$PATH
export PERL5LIB=/opt/%PROJECT%/bin/mri/uploadNeuroDB:/opt/%PROJECT%/bin/mri/dicom-archive:$PERL5LIB
export PATH=/opt/${PROJECT}/bin/mri:/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/uploadNeuroDB/bin:/opt/${PROJECT}/bin/mri/dicom-archive:/opt/${PROJECT}/bin/mri/python:/opt/${PROJECT}/bin/mri/tools:/opt/${PROJECT}/bin/mri/python/react-series-data-viewer:${MINC_TOOLKIT_DIR}/bin:/usr/local/bin/tpcclib:$PATH
export PERL5LIB=/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/dicom-archive:$PERL5LIB
export TMPDIR=/tmp
export LORIS_CONFIG=/opt/%PROJECT%/bin/mri/dicom-archive
export LORIS_CONFIG=/opt/${PROJECT}/bin/mri/dicom-archive

# for the Python scripts
export LORIS_MRI=/opt/%PROJECT%/bin/mri
export PYTHONPATH=$PYTHONPATH:/opt/%PROJECT%/bin/mri/python:/opt/%PROJECT%/bin/mri/python/react-series-data-viewer
source /opt/%PROJECT%/bin/mri/python_virtualenvs/loris-mri-python/bin/activate
export LORIS_MRI=/opt/${PROJECT}/bin/mri
export PYTHONPATH=$PYTHONPATH:/opt/${PROJECT}/bin/mri/python:/opt/${PROJECT}/bin/mri/python/react-series-data-viewer
source /opt/${PROJECT}/bin/mri/python_virtualenvs/loris-mri-python/bin/activate

# for the defacing scripts
export BEASTLIB=%MINC_TOOLKIT_DIR%/../share/beast-library-1.1
export MNI_MODELS=%MINC_TOOLKIT_DIR%/../share/icbm152_model_09c
export BEASTLIB=${MINC_TOOLKIT_DIR}/../share/beast-library-1.1
export MNI_MODELS=${MINC_TOOLKIT_DIR}/../share/icbm152_model_09c
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