From 91ca149b9d016a75e684f39a6cfc693cac6f20ed Mon Sep 17 00:00:00 2001 From: kongtiaowang Date: Mon, 22 Apr 2024 15:20:54 -0400 Subject: [PATCH] environment logic change --- environment | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/environment b/environment index 50d3064c0..029d1103c 100644 --- a/environment +++ b/environment @@ -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