AFNI/TORTOISE

Compute Resources

• Have questions or need help with compute, including activation or issues? Follow this link.

• User Agreement

Docker Usage

• The information contained on this page assumes that you have a knowledge base of using Docker to create images and push them to a repository for use. If you need to review that information, please see the links below.

• Docker and the RIS Compute Service

• Docker Basics: Building, Tagging, & Pushing A Custom Docker Image

Image Details

• Docker image hosted at gcr.io/ris-registry-shared/afni-tortoise.

• Versions Available:

  • latest, v3.2.0

  • v3.1.4

• Software Included

  • AFNI

  • TORTOISE, comprised of the following tools:

    • DIFFPREP

    • DRBUDDI

    • DIFFCALC - CLI version

    • DRTAMAS

  • R Packages

  • GUI is not currently included in this image

Requirements for Usage in RIS

Initial Setup

• An initial setup of dependent files and directory structure in your compute home directory is required.

Note

• Setup will create/modify the following in the compute home directory: .afni/, .afnirc, .bashrc, .sumarc.

• In rare cases, $HOME is not /home/wustlkey. See the RIS Compute Quick Start for details. If this is the case, enter echo $HOME and insert the result at the appropriate places below.

• Connect to compute and run the following, adjusting for individual compute username, home location, etc.

  LSF_DOCKER_VOLUMES='/home/wustlkey:/home/wustlkey' PATH=/home/wustlkey:/linux_centos_7_64:$PATH
  bsub -q general-interactive -Is -a 'docker(gcr.io/ris-registry-shared/afni-tortoise)' /bin/bash -c "cp /linux_centos_7_64/AFNI.afnirc ~/.afnirc; suma -update_env; apsearch -update_all_afni_help; /bin/bash"
  

Note

• If you are a member of more than one compute group, you will be prompted to specify an LSF User Group with -G group_name or by setting the LSB_SUB_USER_GROUP variable.

• Paste the following in its entirety and run to append the .bashrc file.

cat <<EOF >> $HOME/.bashrc
ahdir=`apsearch -afni_help_dir`
if [ -f "$ahdir/all_progs.COMP.bash" ]
then
    . $ahdir/all_progs.COMP.bash
fi
export R_LIBS=/usr/local/lib/R/library/’
EOF

• Update shell.

. ~/.bashrc

Run on LSF

• Connect to compute and run the following, adjusting for individual parameters and replacing <tag> with the appropriate version.

LSF_DOCKER_VOLUMES='/home/wustlkey:/home/wustlkey' PATH=/home/wustlkey:/linux_centos_7_64:$PATH
bsub -q general-interactive -Is -a 'docker(gcr.io/ris-registry-shared/afni-tortoise:<tag>)' /bin/bash