diff --git a/Dockerfile b/Dockerfile index 6df16a12..6f84f795 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ # Ubuntu 20.04 LTS -FROM ubuntu:focal +FROM ubuntu:focal-20210827 ENV DEBIAN_FRONTEND="noninteractive" \ LANG="en_US.UTF-8" \ LC_ALL="en_US.UTF-8" @@ -38,7 +38,7 @@ RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca RUN apt-get update && \ apt-get install -y --no-install-recommends \ connectome-workbench=1.5.0-1~nd20.04+1 \ - git-annex-standalone=8.20210223-1~ndall+1 && \ + git-annex-standalone=8.20210903-1~ndall+1 && \ apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* # Installing ANTs 2.3.4 (NeuroDocker build) @@ -85,7 +85,19 @@ RUN apt-get update -qq \ && echo "Downloading AFNI ..." \ && mkdir -p /opt/afni-latest \ && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \ - | tar -xz -C /opt/afni-latest --strip-components 1 + | tar -xz -C /opt/afni-latest --strip-components 1 \ + --exclude "linux_openmp_64/*.gz" \ + --exclude "linux_openmp_64/funstuff" \ + --exclude "linux_openmp_64/shiny" \ + --exclude "linux_openmp_64/afnipy" \ + --exclude "linux_openmp_64/lib/RetroTS" \ + --exclude "linux_openmp_64/meica.libs" \ + # Keep only what we use + && find /opt/afni-latest -type f -not \( \ + -name "3dTshift" -or \ + -name "3dUnifize" -or \ + -name "3dAutomask" -or \ + -name "3dvolreg" \) -delete ENV PATH="/opt/afni-latest:$PATH" \ AFNI_IMSAVE_WARNINGS="NO" \ AFNI_PLUGINPATH="/opt/afni-latest" @@ -94,7 +106,10 @@ ENV PATH="/opt/afni-latest:$PATH" \ RUN echo "Downloading Convert3D ..." \ && mkdir -p /opt/convert3d-1.0.0 \ && curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download \ - | tar -xz -C /opt/convert3d-1.0.0 --strip-components 1 + | tar -xz -C /opt/convert3d-1.0.0 --strip-components 1 \ + --exclude "c3d-1.0.0-Linux-x86_64/lib" \ + --exclude "c3d-1.0.0-Linux-x86_64/share" \ + --exclude "c3d-1.0.0-Linux-x86_64/bin/c3d_gui" ENV C3DPATH="/opt/convert3d-1.0.0" \ PATH="/opt/convert3d-1.0.0/bin:$PATH" @@ -125,8 +140,50 @@ RUN apt-get update -qq \ && mkdir -p /opt/fsl-5.0.11 \ && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-centos6_64.tar.gz \ | tar -xz -C /opt/fsl-5.0.11 --strip-components 1 \ - && echo "Installing FSL conda environment ..." \ - && bash /opt/fsl-5.0.11/etc/fslconf/fslpython_install.sh -f /opt/fsl-5.0.11 + --exclude "fsl/config" \ + --exclude "fsl/data/atlases" \ + --exclude "fsl/data/first" \ + --exclude "fsl/data/mist" \ + --exclude "fsl/data/possum" \ + --exclude "fsl/data/standard/bianca" \ + --exclude "fsl/data/standard/tissuepriors" \ + --exclude "fsl/doc" \ + --exclude "fsl/etc/default_flobs.flobs" \ + --exclude "fsl/etc/fslconf" \ + --exclude "fsl/etc/js" \ + --exclude "fsl/etc/luts" \ + --exclude "fsl/etc/matlab" \ + --exclude "fsl/extras" \ + --exclude "fsl/include" \ + --exclude "fsl/python" \ + --exclude "fsl/refdoc" \ + --exclude "fsl/src" \ + --exclude "fsl/tcl" \ + --exclude "fsl/bin/FSLeyes" \ + && find /opt/fsl-5.0.11/bin -type f -not \( \ + -name "applywarp" -or \ + -name "bet" -or \ + -name "bet2" -or \ + -name "convert_xfm" -or \ + -name "fast" -or \ + -name "flirt" -or \ + -name "fsl_regfilt" -or \ + -name "fslhd" -or \ + -name "fslinfo" -or \ + -name "fslmaths" -or \ + -name "fslmerge" -or \ + -name "fslroi" -or \ + -name "fslsplit" -or \ + -name "fslstats" -or \ + -name "imtest" -or \ + -name "mcflirt" -or \ + -name "melodic" -or \ + -name "prelude" -or \ + -name "remove_ext" -or \ + -name "susan" -or \ + -name "topup" -or \ + -name "zeropad" \) -delete \ + && find /opt/fsl-5.0.11/data/standard -type f -not -name "MNI152_T1_2mm_brain.nii.gz" -delete ENV FSLDIR="/opt/fsl-5.0.11" \ PATH="/opt/fsl-5.0.11/bin:$PATH" \ FSLOUTPUTTYPE="NIFTI_GZ" \ @@ -232,6 +289,7 @@ RUN conda install -y python=3.8 \ mkl-service=2.3 \ numpy=1.20 \ scipy=1.6 \ + scikit-image=0.18 \ scikit-learn=0.24 \ matplotlib=3.3 \ pandas=1.2 \ @@ -271,7 +329,7 @@ ARG VCS_REF ARG VERSION LABEL org.label-schema.build-date=$BUILD_DATE \ org.label-schema.name="nibabies" \ - org.label-schema.description="nibabies - NeuroImaging tools for infants" \ + org.label-schema.description="nibabies - NeuroImaging tools for babies" \ org.label-schema.url="https://github.com/nipreps/nibabies" \ org.label-schema.vcs-ref=$VCS_REF \ org.label-schema.vcs-url="https://github.com/nipreps/nibabies" \