sing

Singularity.v0.0.1

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+Bootstrap: docker
+From: ubuntu:20.04
+
+%help
+  Registration of PET images. Info and usage:
+    /opt/petreg/README.md
+
+
+%setup
+  mkdir -p ${SINGULARITY_ROOTFS}/opt/petreg
+
+
+%files
+  src                          /opt/petreg
+  README.md                    /opt/petreg
+
+
+%labels
+  Maintainer [email protected]
+
+
+%post
+  apt-get update > /dev/null 2>&1
+  apt-get install -y wget unzip zip xvfb ghostscript imagemagick bc > /dev/null 2>&1   # Misc tools
+  apt-get install -y libopenblas-base language-pack-en              > /dev/null 2>&1   # FSL
+
+  # Fix imagemagick policy to allow PDF output and text read. See https://usn.ubuntu.com/3785-1/
+  sed -i 's/rights="none" pattern="PDF"/rights="read | write" pattern="PDF"/' \
+    /etc/ImageMagick-6/policy.xml
+  sed -i 's/rights="none" pattern="@\*"/rights="read" pattern="@*"/' \
+    /etc/ImageMagick-6/policy.xml
+
+  # FSL. We need 6.0.4 for the b02b01_1.sch topup schedule. See
+  # https://fsl.fmrib.ox.ac.uk/fsldownloads/manifest.csv
+  # And, the centos7 version suits for Ubuntu 14-20.
+  fslver=6.0.4
+  cd /usr/local
+  wget -nv https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-${fslver}-centos7_64.tar.gz
+  tar -zxf fsl-${fslver}-centos7_64.tar.gz
+  rm fsl-${fslver}-centos7_64.tar.gz
+
+  # FSL setup
+  export FSLDIR=/usr/local/fsl
+  . ${FSLDIR}/etc/fslconf/fsl.sh
+  export PATH=${FSLDIR}/bin:${PATH}
+
+  # Run the FSL python installer. A clue that we forgot this is an imglob error at runtime
+  ${FSLDIR}/etc/fslconf/fslpython_install.sh
+
+  # Create input/output directories for binding
+  mkdir /INPUTS && mkdir /OUTPUTS && mkdir /wkdir
+
+
+%environment
+
+  # FSL
+  export FSLDIR=/usr/local/fsl
+
+  # Path
+  export PATH=/opt/petreg/src:/usr/local/fsl/bin:${PATH}
+
+
+%runscript
+  xwrapper.sh "$@"
+