Skip to content

Commit

Permalink
Merge branch 'develop'
Browse files Browse the repository at this point in the history
  • Loading branch information
perronea committed Mar 1, 2021
2 parents e480a8f + b30f97c commit ed7941c
Show file tree
Hide file tree
Showing 6 changed files with 125 additions and 134 deletions.
109 changes: 32 additions & 77 deletions Dockerfile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -76,26 +76,28 @@ RUN apt-get clean \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker

# install wb_command v1.3.2
#-----------------------------
# Install Connectome Workbench
#-----------------------------
RUN mkdir -p /opt
WORKDIR /opt
RUN curl --retry 5 https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.3.2.zip --output workbench-linux64-v1.3.2.zip && \
unzip workbench-linux64-v1.3.2.zip && \
rm workbench-linux64-v1.3.2.zip
RUN curl --retry 5 https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.4.2.zip --output workbench-linux64-v1.4.2.zip && \
unzip workbench-linux64-v1.4.2.zip && \
rm workbench-linux64-v1.4.2.zip

#-------------------
# Install ANTs 2.2.0
#-------------------
#-------------
# Install ANTs
#-------------
RUN echo "Downloading ANTs ..." \
&& curl -sSL --retry 5 https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz \
| tar zx -C /opt

ENV ANTSPATH=/opt/ants \
PATH=/opt/ants:$PATH

#------------------------
# Install Convert3D 1.0.0
#------------------------
#------------------
# Install Convert3D
#------------------
RUN echo "Downloading C3D ..." \
&& mkdir /opt/c3d \
&& curl -sSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download \
Expand All @@ -108,9 +110,9 @@ RUN echo "Downloading C3D ..." \
ENV C3DPATH=/opt/c3d/bin \
PATH=/opt/c3d/bin:$PATH

#--------------------------
# Install FreeSurfer v5.3.0-HCP
#--------------------------
#-------------------
# Install FreeSurfer
#-------------------
RUN echo "Downloading FreeSurfer ..." \
&& curl -sSL --retry 5 https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP.tar.gz \
| tar xz -C /opt \
Expand All @@ -133,7 +135,7 @@ ENV FREESURFER_HOME=/opt/freesurfer
RUN chmod 777 /opt/freesurfer

#-----------------------------------------------------------
# Install FSL v5.0.10
# Install FSL
# FSL is non-free. If you are considering commerical use
# of this Docker image, please consult the relevant license:
# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
Expand All @@ -158,16 +160,16 @@ ENV FSLDIR=/opt/fsl \
FSL_DIR=/opt/fsl \
PATH=/opt/fsl/bin:$PATH

#---------------------
#--------------------------------
# Install MATLAB Compiler Runtime
#---------------------
#--------------------------------
RUN mkdir /opt/matlab /opt/matlab_download
WORKDIR /opt/matlab_download
RUN wget http://ssd.mathworks.com/supportfiles/downloads/R2016b/deployment_files/R2016b/installers/glnxa64/MCR_R2016b_glnxa64_installer.zip \
&& unzip MCR_R2016b_glnxa64_installer.zip \
RUN wget http://ssd.mathworks.com/supportfiles/downloads/R2017a/deployment_files/R2017a/installers/glnxa64/MCR_R2017a_glnxa64_installer.zip \
&& unzip MCR_R2017a_glnxa64_installer.zip \
&& ./install -agreeToLicense yes -mode silent -destinationFolder /opt/matlab \
&& rm -rf /opt/matlab_download
#ENV LD_LIBRARY_PATH=/opt/matlab/v91/bin/glnxa64:/opt/matlab/v91/glnxa64:/opt/matlab/v91/runtime/glnxa64:$LD_LIBRARY_PATH
#ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/matlab/v91/bin/glnxa64:/opt/matlab/v91/glnxa64:/opt/matlab/v91/runtime/glnxa64

#---------------------
# Install MSM Binaries
Expand All @@ -178,9 +180,9 @@ RUN mv /opt/homes/ecr05/MSM_HOCR_v2/* /opt/msm/
RUN rm -rf /opt/homes /opt/msm/MacOSX /opt/msm/Centos
ENV MSMBINDIR=/opt/msm/Ubuntu

#----------------------------
# Make perl version 5.20.3
#----------------------------
#----------
# Make perl
#----------
RUN curl -sSL --retry 5 http://www.cpan.org/src/5.0/perl-5.20.3.tar.gz | tar zx -C /opt
WORKDIR /opt/perl-5.20.3
RUN ./Configure -des -Dprefix=/usr/local
Expand All @@ -189,17 +191,17 @@ RUN rm -f /usr/bin/perl && ln -s /usr/local/bin/perl /usr/bin/perl
WORKDIR /
RUN rm -rf /opt/perl-5.20.3/

#------------------
#---------------
# Make libnetcdf
#------------------
#---------------

RUN curl -sSL --retry 5 ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.6.1.tar.gz | tar zx -C /opt
WORKDIR /opt/netcdf-4.6.1/
RUN curl -sSL --retry 5 https://github.com/Unidata/netcdf-c/archive/v4.6.1.tar.gz | tar zx -C /opt
WORKDIR /opt/netcdf-c-4.6.1/
RUN LDFLAGS=-L/usr/local/lib && CPPFLAGS=-I/usr/local/include && ./configure --disable-netcdf-4 --disable-dap --enable-shared --prefix=/usr/local
RUN make && make install
WORKDIR /usr/local/lib
RUN ln -s libnetcdf.so.13.1.1 libnetcdf.so.6
RUN rm -rf /opt/netcdf-4.6.1/
RUN rm -rf /opt/netcdf-c-4.6.1/
ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

#------------------------------------------
Expand All @@ -219,21 +221,21 @@ ENV WORKBENCHDIR=/opt/workbench \
RUN ln -s -f /lib/x86_64-linux-gnu/libz.so.1.2.11 /opt/workbench/libs_linux64/libz.so.1

# Fix libstdc++6 error
RUN ln -sf /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.24 /opt/matlab/v91/sys/os/glnxa64/libstdc++.so.6
RUN ln -sf /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.24 /opt/matlab/v92/sys/os/glnxa64/libstdc++.so.6

# add dcan dependencies
RUN mkdir /opt/dcan-tools
WORKDIR /opt/dcan-tools
# dcan hcp code
RUN git clone -b 'v2.0.0' --single-branch --depth 1 https://github.com/DCAN-Labs/DCAN-HCP.git /opt/pipeline
# dcan bold processing
RUN git clone -b 'v4.0.0' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan_bold_processing.git dcan_bold_proc
RUN git clone -b 'hotfix/issue27' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan_bold_processing.git dcan_bold_proc
# dcan custom clean
RUN git clone -b 'v0.0.0' --single-branch --depth 1 https://github.com/DCAN-Labs/CustomClean.git customclean
# abcd task prep
RUN git clone -b 'v0.0.0' --single-branch --depth 1 https://github.com/DCAN-Labs/abcd_task_prep.git ABCD_tfMRI
# dcan executive summary
RUN git clone -b 'v0.0.0' --single-branch --depth 1 https://github.com/DCAN-Labs/ExecutiveSummary.git executivesummary
RUN git clone -b 'v0.0.1' --single-branch --depth 1 https://github.com/DCAN-Labs/ExecutiveSummary.git executivesummary
# unzip template file
RUN gunzip /opt/dcan-tools/executivesummary/summary_tools/templates/parasagittal_Tx_169_template.scene.gz

Expand All @@ -255,50 +257,3 @@ COPY ["LICENSE", "/LICENSE"]
ENTRYPOINT ["/entrypoint.sh"]
WORKDIR /
CMD ["--help"]

#--------------------------------------
# Save container specifications to JSON
#--------------------------------------
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "check_urls": true, \
\n "instructions": [ \
\n [ \
\n "base", \
\n "ubuntu:17.10" \
\n ], \
\n [ \
\n "workbench", \
\n { \
\n "version": "1.3.2" \
\n } \
\n ], \
\n [ \
\n "ants", \
\n { \
\n "version": "2.2.0" \
\n } \
\n ], \
\n [ \
\n "c3d", \
\n { \
\n "version": "1.0.0" \
\n } \
\n ], \
\n [ \
\n "freesurfer", \
\n { \
\n "version": "5.3.0-HCP", \
\n "license_path": "license.txt" \
\n } \
\n ], \
\n [ \
\n "fsl", \
\n { \
\n "version": "5.0.10" \
\n } \
\n ] \
\n ], \
\n "generation_timestamp": "2018-03-15 20:22:57", \
\n "neurodocker_version": "0.3.2-9-g7441d77" \
\n}' > /neurodocker/neurodocker_specs.json
4 changes: 2 additions & 2 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -113,8 +113,8 @@ optional arguments:
quartile range for participant group respiratory rate
(breaths per minute), or to match bids physio data
directly [3]. These parameters are highly recommended
for data acquired with a frequency of approx. 1 Hz or
more (TR<=1.0). Default is no filter.
for data acquired with a frequency of greater than 1
Hz (TR less than 1 second). Default is no filter.
Special pipeline options:
Options which pertain to an alternative pipeline or an extra stage which is not
Expand Down
2 changes: 1 addition & 1 deletion app/SetupEnv.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ export MSMBINDIR=/opt/msm/Ubuntu


# Set up DCAN Environment Variables
export MCRROOT=/opt/matlab/v91
export MCRROOT=/opt/matlab/v92
export DCANBOLDPROCDIR=/opt/dcan-tools/dcan_bold_proc
export DCANBOLDPROCVER=DCANBOLDProc_v4.0.0
export EXECSUMDIR=/opt/dcan-tools/executivesummary
Expand Down
Loading

0 comments on commit ed7941c

Please sign in to comment.