update dependencies;

new merged sequence and julia
NeuroDesk · Sep 28, 2023 · a797655 · a797655
1 parent 6b3203e
commit a797655
Show file tree

Hide file tree

Showing 3 changed files with 37 additions and 42 deletions.
diff --git a/recipes/mrsiproc/README.md b/recipes/mrsiproc/README.md
@@ -1,19 +1,16 @@
 
 ----------------------------------
-## mrsiproc/0.0.1 ##
+## mrsiproc/toolVersion ##
 
 Includes the following:  
-##### -- OS: Ubuntu 20.04 (Built off Matlab 2022a Deep learning Docker)
+##### -- OS: Ubuntu 20.04 (Built from fsl neurodocker)
 ##### -- Minc 						(Version 1.9.15)
-##### -- MATLAB 					(Version R2021b)
+##### -- MATLAB Runtime		(Version R2021b)
 ##### -- HD-BET           (Version 1.0)
-##### -- tar
-##### -- gzip
-##### -- gunzip
 ##### -- LCModel 					(Version 6.3.1)
-##### -- dcm2nii
+##### -- dcm2niix
 ##### -- Python           (Version 3.10)
-##### -- Julia            (Version 1.9.0-rc2)
+##### -- Julia            (Version 1.9.3)
 
 
 Overview
@@ -61,7 +58,7 @@ Run MRSI scripts
 -----------------------------------------
 Run the scripts from within a singularity shell inside Neurodesk. Example:
 ```bash
-singularity shell singularity shell /cvmfs/neurodesk.ardc.edu.au/containers/mrsiproc_0.0.1_20221026/mrsiproc_0.0.1_20221026.simg
+singularity shell singularity shell /cvmfs/neurodesk.ardc.edu.au/containers/mrsiproc_toolVersion_20221026/mrsiproc_toolVersion_20221026.simg
 ```
 ```bash
 Singularity> cd /neurodesktop-storage/mrsi_proc
@@ -71,7 +68,7 @@ Singularity> ./Run_MRSI_test.sh
 To run applications outside of this container
 ---------------------------------------------
   (This is not working yet)  
-  ml mrsiproc/0.0.1
+  ml mrsiproc/toolVersion
 
 Citation
 --------

diff --git a/recipes/mrsiproc/build.sh b/recipes/mrsiproc/build.sh
@@ -4,15 +4,15 @@ set -e
 # this template file builds datalad and is then used as a docker base image for layer caching + it contains examples for various things like github install, curl, ...
 export toolName='mrsiproc'
 export toolVersion='0.0.1' # the version number cannot contain a "-" - try to use x.x.x notation always
-export matlabVersion='2021b' # compatible with MATLAB.jl (julia)
+export matlabVersion='2021b' # this has to match the version on which the matlab scripts were compiled
+export matlabUpdateVersion='6'
 export mincVersion='1.9.15'
 export lcmodelVersion='6.3'
 export hdbetVersion='1.0' # note the hdbet doesn't really have a version
-export fslVersion='6.0.5.1'
-export pythonVersion='py310'
-export minicondaVersion='23.3.1-0'
-export dcm2niiVersion='003f0d19f1e57b0129c9dcf3e653f51ca3559028' # copied from qsmxt
-export juliaVersion='1.9.0-rc3'
+export fslVersion='6.0.7.1'
+export minicondaVersion='latest'
+export dcm2niixVersion='003f0d19f1e57b0129c9dcf3e653f51ca3559028' # copied from qsmxt
+export juliaVersion='1.9.3'
 
 # Don't forget to update version change in README.md!!!!!
 # toolName or toolVersion CANNOT contain capital letters or dashes or underscores (Docker registry does not accept this!)
@@ -35,11 +35,11 @@ source ../main_setup.sh
 # NOTE 2: THE BACKSLASH (\) AT THE END OF EACH LINE MUST FOLLOW THE COMMENT. A BACKSLASH BEFORE THE COMMENT WON'T WORK!
 ##########################################################################################################################################
 neurodocker generate ${neurodocker_buildMode} \
-   --base-image vnmd/fsl_${fslVersion}:20221016 \
+   --base-image vnmd/fsl_${fslVersion} \
    --pkg-manager apt \
    --env DEPLOY_PATH=/opt/${toolName}-${toolVersion}/bin/ \
    --user=root `# otherwise some permission denied error occurs during docker build` \
-   --dcm2niix method=source version=${dcm2niiVersion} \
+   --dcm2niix method=source version=${dcm2niixVersion} \
    --minc version=${mincVersion} \
    \
    --install wget curl git ca-certificates ltrace strace libxml2 gcc build-essential gzip tar unzip datalad libfftw3-3 software-properties-common bc `# install apt-get packages` \
@@ -49,7 +49,7 @@ neurodocker generate ${neurodocker_buildMode} \
       && dpkg -i libjpeg62-turbo_2.0.6-4_amd64.deb \
       && rm libjpeg62-turbo_2.0.6-4_amd64.deb" `# LIBJPEGTURBO_6.2 is required by dcm2mnc` \
    \
-   --miniconda version=${pythonVersion}_${minicondaVersion} \
+   --miniconda version=${minicondaVersion} \
    \
    --workdir /opt `# HD-BET` \
    --run="git clone https://github.com/MIC-DKFZ/HD-BET" \
@@ -63,7 +63,6 @@ neurodocker generate ${neurodocker_buildMode} \
    --run="curl -o /opt/HD-BET/hd-bet_params/3.model https://zenodo.org/record/2540695/files/3.model?download=1" \
    --run="curl -o /opt/HD-BET/hd-bet_params/4.model https://zenodo.org/record/2540695/files/4.model?download=1" \
    --run="pip install -e ." \
-   --env DEPLOY_BINS=hd-bet \
    \
    --workdir=/opt/lcmodel-${lcmodelVersion}/ `# install LCModel and things to make it work ` \
    --install curl ca-certificates libxft2 libxss1 libnet-ifconfig-wrapper-perl vim nano unzip gv unrar `# LCModel dependencies (libtk8.6 removed asks interactive question)` \
@@ -99,39 +98,34 @@ neurodocker generate ${neurodocker_buildMode} \
    --copy gui-defaults  /opt/lcmodel-${lcmodelVersion}/.lcmodel/profiles/1/gui-defaults \
    --run="chmod a+rwx /opt/lcmodel-${lcmodelVersion} -R" \
    --env DEPLOY_PATH=/opt/lcmodel-${lcmodelVersion}/.lcmodel/bin/:/opt/lcmodel-${lcmodelVersion}/.lcmodel/ \
-   --env PATH=/opt/lcmodel-${lcmodelVersion}/.lcmodel/bin/:/opt/lcmodel-${lcmodelVersion}/.lcmodel/:'$PATH' \
+   --env PATH="\${PATH}:/opt/lcmodel-${lcmodelVersion}/.lcmodel/bin/:/opt/lcmodel-${lcmodelVersion}/.lcmodel/" \
    \
-   --workdir /opt `# Add Julia` \
+   `# Add MATLAB compiler runtime (doesn't need license)` \
+   --install bc curl libncurses5 libxext6 libxmu6 libxpm-dev libxt6 unzip openjdk-8-jre dbus-x11 \
+   --run="wget https://ssd.mathworks.com/supportfiles/downloads/R${matlabVersion}/Release/${matlabUpdateVersion}/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_R${matlabVersion}_Update_${matlabUpdateVersion}_glnxa64.zip && \
+          unzip MATLAB_Runtime_R${matlabVersion}_Update_${matlabUpdateVersion}_glnxa64.zip -d mcrtmp && \
+          mcrtmp/install -mode silent -destinationFolder /opt/MATLAB_Runtime_R${matlabVersion} -agreeToLicense yes && \
+          rm -rf mcrtmp && \
+          rm -f MATLAB_Runtime_R${matlabVersion}_Update_${matlabUpdateVersion}_glnxa64.zip" \
+   \
+   --env LD_LIBRARY_PATH="\${LD_LIBRARY_PATH}:/opt/MATLAB_Runtime_R${matlabVersion}/R${matlabVersion}/runtime/glnxa64:/opt/MATLAB_Runtime_R${matlabVersion}/R${matlabVersion}/bin/glnxa64:/opt/MATLAB_Runtime_R${matlabVersion}/R${matlabVersion}/sys/os/glnxa64:/opt/MATLAB_Runtime_R${matlabVersion}/R${matlabVersion}/extern/bin/glnxa64" \
+   --workdir /opt `# Add Julia with MRSI packages` \
    --run="wget https://julialang-s3.julialang.org/bin/linux/x64/${juliaVersion:0:3}/julia-${juliaVersion}-linux-x86_64.tar.gz && \
       tar zxvf julia-${juliaVersion}-linux-x86_64.tar.gz && \
       rm -rf julia-${juliaVersion}-linux-x86_64.tar.gz" \
-   --env PATH='$PATH':/opt/julia-${juliaVersion}/bin \
    --env JULIA_DEPOT_PATH=/opt/julia_depot \
+   --env PATH="\${PATH}:/opt/julia-${juliaVersion}/bin" \
+   --copy install_packages.jl "/opt" \
+   --env JULIA_DEPOT_PATH="/opt/julia_depot" \
+   --run="julia install_packages.jl" \
+   --env JULIA_DEPOT_PATH="~/.julia:/opt/julia_depot" \
    \
-   `# Add MATLAB compiler runtime (doesn't need license)` \
-   --install bc curl libncurses5 libxext6 libxmu6 libxpm-dev libxt6 multiarch-support unzip openjdk-8-jre dbus-x11 \
-   --run="wget https://ssd.mathworks.com/supportfiles/downloads/R${matlabVersion}/Release/6/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_R${matlabVersion}_Update_6_glnxa64.zip && \
-          unzip MATLAB_Runtime_R${matlabVersion}_Update_6_glnxa64.zip -d mcrtmp && \
-          mcrtmp/install -mode silent -destinationFolder /opt/MATLAB_Runtime_R${matlabVersion} -agreeToLicense yes && \
-          rm -rf mcrtmp && \
-          rm -f MATLAB_Runtime_R${matlabVersion}_Update_6_glnxa64.zip" \
+   --env DEPLOY_BINS="julia:python:dcm2niix:hd-bet:lcmodel:nii2mnc:bet:fsl" \
    \
    --copy README.md /README.md                          `# include README file in container` \
    \
   > ${imageName}.${neurodocker_buildExt}                `# LAST COMMENT; NOT FOLLOWED BY BACKSLASH!`
 
-## To add in future version
-   #--matlabmcr version=2023a                `# Add MATLAB runtime for compiled MATLAB code without license` \ doesn't work for some reason..
-   #--run "export MatlabFunctionsFolder=/opt/mrsiproc/matlab/MatlabFunctions"  `#export dir for matlab scripts` \
-   #--run "mkdir -p /opt/mrsiproc/matlab/MatlabFunctions" \
-   #--run "chmod a+rwx /opt/mrsiproc/matlab/ -R"  `#setup script dir for matlab functions and assorted scripts` \
-   #--run "git clone insert/https/here"
-   #--copy ./run_scripts/*mat /opt/mrsiproc/matlab/MatlabFunctions/ \
-   #--copy ./run_scripts/*m /opt/mrsiproc/matlab/MatlabFunctions/ \
-   #--copy ./run_scripts/*sh /opt/mrsiproc/ \
-   #--run "chmod a+rwx /opt/mrsiproc/ -R" \
-   #--run "/opt/mrsiproc/startup_matlab.sh" \
-
 if [ "$1" != "" ]; then
    ./../main_build.sh
 fi
diff --git a/recipes/mrsiproc/install_packages.jl b/recipes/mrsiproc/install_packages.jl
@@ -0,0 +1,4 @@
+import Pkg
+packages = ["MAT", "Comonicon"]
+Pkg.add(packages)
+Pkg.add(Pkg.PackageSpec(url="https://github.com/korbinian90/MRSI.jl"))