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neurodocker_cmd.sh
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neurodocker_cmd.sh
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#!/bin/bash
neurodocker \
generate singularity \
--base=neurodebian:stretch \
--pkg-manager=apt \
--install wget r-cran-afex r-cran-car \
--fsl version=5.0.11 \
--convert3d version=1.0.0 method=binaries \
--afni version=latest install_r=true install_r_pkgs=true \
--ants version=2.2.0 \
--convert3d version=nightly \
--env XCPEDIR=/xcpEngine-master FSLDIR=/opt/fsl-5.0.11 \
AFNI_PATH=/opt/afni-latest C3D_PATH=/opt/convert3d-nightly/bin \
--add-to-entrypoint 'export XCPEDIR=/xcpEngine-master' \
--add-to-entrypoint 'export FSLDIR=/opt/fsl-5.0.11' \
--add-to-entrypoint 'export AFNI_PATH=/opt/afni-latest' \
--add-to-entrypoint 'export C3D_PATH=/opt/convert3d-nightly/bin' \
--add-to-entrypoint 'export ANTSPATH=/opt/ants-2.2.0' \
--add-to-entrypoint 'export PATH=$PATH:$XCPEDIR' \
--run-bash 'cd / && wget https://github.com/PennBBL/xcpEngine/archive/master.zip && unzip master.zip' \
--run-bash 'XCPEDIR=/xcpEngine-master FSLDIR=/opt/fsl-5.0.11 AFNI_PATH=/opt/afni-latest C3D_PATH=/opt/convert3d-nightly/bin ANTSPATH=/opt/ants-2.2.0 /xcpEngine-master/xcpReset' \
--run-bash 'export PATH=/opt/afni-latest:$PATH && rPkgsInstall -pkgs ALL && rPkgsInstall -pkgs optparse,pracma,RNifti,svglite,signal,reshape2,ggplot2,lme4' \
--run-bash ' echo ==========================' \
--run-bash 'cat $ND_ENTRYPOINT' \
--run-bash ' echo ==========================' \
--entrypoint '/neurodocker/startup.sh /xcpEngine-master/xcpEngine "$@"' > Singularity
neurodocker \
generate docker \
--base=neurodebian:stretch \
--pkg-manager=apt \
--install wget \
--fsl version=5.0.11 \
--convert3d version=1.0.0 method=binaries \
--afni version=latest install_r=true install_r_pkgs=true \
--ants version=2.2.0 \
--convert3d version=nightly \
--env XCPEDIR=/xcpEngine-master FSLDIR=/opt/fsl-5.0.11 \
AFNI_PATH=/opt/afni-latest C3D_PATH=/opt/convert3d-nightly/bin \
--add-to-entrypoint 'export XCPEDIR=/xcpEngine-master' \
--add-to-entrypoint 'export FSLDIR=/opt/fsl-5.0.11' \
--add-to-entrypoint 'export AFNI_PATH=/opt/afni-latest' \
--add-to-entrypoint 'export C3D_PATH=/opt/convert3d-nightly/bin' \
--add-to-entrypoint 'export ANTSPATH=/opt/ants-2.2.0' \
--add-to-entrypoint 'export PATH=$PATH:$XCPEDIR' \
--run-bash 'cd / && wget https://github.com/PennBBL/xcpEngine/archive/master.zip && unzip master.zip' \
--run-bash 'XCPEDIR=/xcpEngine-master FSLDIR=/opt/fsl-5.0.11 AFNI_PATH=/opt/afni-latest C3D_PATH=/opt/convert3d-nightly/bin ANTSPATH=/opt/ants-2.2.0 /xcpEngine-master/xcpReset' \
--run-bash 'export PATH=/opt/afni-latest:$PATH && rPkgsInstall -pkgs ALL && rPkgsInstall -pkgs optparse,pracma,RNifti,svglite,signal,reshape2,ggplot2,lme4' \
--run-bash ' echo ==========================' \
--run-bash 'cat $ND_ENTRYPOINT' \
--run-bash ' echo ==========================' \
--entrypoint '/neurodocker/startup.sh /xcpEngine-master/xcpEngine "$@"' > Dockerfile