diff --git a/Dockerfile b/Dockerfile index 706844b..3672591 100644 --- a/Dockerfile +++ b/Dockerfile @@ -158,24 +158,24 @@ RUN export PATH="$HOME/miniconda-latest/bin:$PATH" \ #### install RABIES -ENV export RABIES_VERSION=0.1.3-dev \ +ENV export RABIES_VERSION=0.2.0 \ export RABIES=$HOME/RABIES-${RABIES_VERSION} \ export PYTHONPATH="${PYTHONPATH}:$RABIES" -RUN export RABIES_VERSION=0.1.3-dev && \ +RUN export RABIES_VERSION=0.2.0 && \ export RABIES=$HOME/RABIES-${RABIES_VERSION} && \ - #mkdir -p temp && \ - #curl -L --retry 5 -o temp/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz && \ - #cd temp && \ - #tar zxf RABIES.tar.gz && \ - #cd .. && \ - #conda env create -f temp/RABIES-${RABIES_VERSION}/rabies_environment.yml && \ - #bash temp/RABIES-${RABIES_VERSION}/install.sh && \ - #rm -r temp && \ - git clone https://github.com/CoBrALab/RABIES && \ - mv RABIES $RABIES && \ - conda env create -f $RABIES/rabies_environment.yml && \ - bash $RABIES/install.sh && \ + mkdir -p temp && \ + curl -L --retry 5 -o temp/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz && \ + cd temp && \ + tar zxf RABIES.tar.gz && \ + cd .. && \ + conda env create -f temp/RABIES-${RABIES_VERSION}/rabies_environment.yml && \ + bash temp/RABIES-${RABIES_VERSION}/install.sh && \ + rm -r temp && \ + #git clone https://github.com/CoBrALab/RABIES && \ + #mv RABIES $RABIES && \ + #conda env create -f $RABIES/rabies_environment.yml && \ + #bash $RABIES/install.sh && \ DSURQE_100micron_labels=${RABIES}/template_files/DSURQE_100micron_labels.nii.gz && \ csv_labels=${RABIES}/template_files/DSURQE_40micron_R_mapping.csv && \ /home/rabies/miniconda-latest/envs/rabies/bin/python ${RABIES}/gen_masks.py $DSURQE_100micron_labels $csv_labels ${RABIES}/template_files/DSURQE_100micron && \ @@ -194,7 +194,7 @@ RUN export FSLDIR="/usr/share/fsl/5.0/" && \ . ${FSLDIR}/etc/fslconf/fsl.sh && \ export PATH="/usr/share/fsl/5.0/bin:$PATH" && \ export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH && \ - export RABIES_VERSION=0.1.3-dev && \ + export RABIES_VERSION=0.2.0 && \ export RABIES=$HOME/RABIES-${RABIES_VERSION} && \ export PATH=$PATH:$RABIES/rabies/shell_scripts && \ echo "#! /home/rabies/miniconda-latest/envs/rabies/bin/python" > ${RABIES}/exec.py && \ @@ -218,4 +218,4 @@ WORKDIR /tmp/ ENV PATH /home/rabies/miniconda-latest/envs/rabies/bin:$PATH RUN /bin/bash -c "source activate rabies" -ENTRYPOINT ["/home/rabies/RABIES-0.1.3-dev/exec.py"] +ENTRYPOINT ["/home/rabies/RABIES-0.2.0/exec.py"] diff --git a/README.md b/README.md index 4021ebb..ffa0eae 100644 --- a/README.md +++ b/README.md @@ -298,17 +298,17 @@ Specify Slice Timing Correction info that is fed to AFNI 3dTshift Provided commonspace atlas files.: --anat_template ANAT_TEMPLATE Anatomical file for the commonspace template. - (default: /home/gabriel/RABIES-0.1.3-dev/rabies/../tem + (default: /home/gabriel/RABIES-0.2.0/rabies/../tem plate_files/DSURQE_40micron_average.nii.gz) --brain_mask BRAIN_MASK Brain mask for the template. (default: /home/gabriel/R - ABIES-0.1.3-dev/rabies/../template_files/DSURQE_100mic + ABIES-0.2.0/rabies/../template_files/DSURQE_100mic ron_mask.nii.gz) --WM_mask WM_MASK White matter mask for the template. (default: /home/ga - briel/RABIES-0.1.3-dev/rabies/../template_files/DSURQE + briel/RABIES-0.2.0/rabies/../template_files/DSURQE _100micron_eroded_WM_mask.nii.gz) --CSF_mask CSF_MASK CSF mask for the template. (default: /home/gabriel/RAB - IES-0.1.3-dev/rabies/../template_files/DSURQE_100micro + IES-0.2.0/rabies/../template_files/DSURQE_100micro n_eroded_CSF_mask.nii.gz) --vascular_mask VASCULAR_MASK Can provide a mask of major blood vessels for @@ -316,10 +316,10 @@ Provided commonspace atlas files.: generated by applying MELODIC ICA and selecting the resulting component mapping onto major veins. (Grandjean et al. 2020, NeuroImage; Beckmann et al. - 2005) (default: /home/gabriel/RABIES-0.1.3-dev/rabies/ + 2005) (default: /home/gabriel/RABIES-0.2.0/rabies/ ../template_files/vascular_mask.nii.gz) --labels LABELS Atlas file with anatomical labels. (default: /home/gab - riel/RABIES-0.1.3-dev/rabies/../template_files/DSURQE_ + riel/RABIES-0.2.0/rabies/../template_files/DSURQE_ 40micron_labels.nii.gz) ``` diff --git a/install.sh b/install.sh index 94b4021..e2133b6 100644 --- a/install.sh +++ b/install.sh @@ -1,23 +1,23 @@ ### setup RABIES execution and DSURQE atlas #will install RABIES in HOME directory -export RABIES_VERSION=0.1.3-dev +export RABIES_VERSION=0.2.0 export RABIES=$HOME/RABIES-${RABIES_VERSION} export PYTHONPATH="${PYTHONPATH}:$RABIES" cd $HOME -#curl -L --retry 5 -o $HOME/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz -#tar zxf $HOME/RABIES.tar.gz -#rm $HOME/RABIES.tar.gz -git clone https://github.com/CoBrALab/RABIES -mv RABIES $RABIES +curl -L --retry 5 -o $HOME/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz +tar zxf $HOME/RABIES.tar.gz +rm $HOME/RABIES.tar.gz +#git clone https://github.com/CoBrALab/RABIES +#mv RABIES $RABIES #creates an executable script to execute rabies mkdir -p $RABIES/bin echo -e '#! /usr/bin/env python \nfrom rabies.run_main import execute_workflow \nexecute_workflow()' > $RABIES/bin/rabies chmod +x $RABIES/bin/rabies echo "# added by RABIES" >> $HOME/.bashrc -echo "export RABIES_VERSION=0.1.3-dev" >> $HOME/.bashrc +echo "export RABIES_VERSION=0.2.0" >> $HOME/.bashrc echo "export RABIES=$RABIES" >> $HOME/.bashrc echo 'export PYTHONPATH="${PYTHONPATH}:$RABIES"' >> $HOME/.bashrc echo 'export PATH=$PATH:$RABIES/bin' >> $HOME/.bashrc diff --git a/rabies/_info.py b/rabies/_info.py index e907a41..ddba5bd 100644 --- a/rabies/_info.py +++ b/rabies/_info.py @@ -1,4 +1,4 @@ -__version__ = "0.1.3-dev" +__version__ = "0.2.0" __packagename__ = 'RABIES' __url__ = 'https://github.com/CoBrALab/'