AFNI/TORTOISE

Owned by RIS-SVC-conf-publish
Last updated: Jun 06, 2023
2 min read

Compute Resources

Docker Usage

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.

  • 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"

  • 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