MarcusChMa / taudem_docker

Up-to-date TauDEM Docker image

taudem_docker

Up-to-date TauDEM Docker image

This TauDEM Docker image includes catchhydrogeo.

The following instructions are for Docker. Instructions for Singularity are below.

TauDEM commands may be run as one-off commands using this Docker image using the following shell command as a template:

docker run --name hand_taudem_bash --rm -i -t --mount type=bind,source="$(pwd)",target="/mnt/host" dhardestylewis/taudem:tacc pitremove -z /mnt/host/DEM.tif -fel /mnt/host/DEMfel.tif

or multiple TauDEM commands may be run in sequence bringing up the Docker image once for all commands using the following shell command as a template:

docker run --name taudem_bash --rm -i -t --mount type=bind,source="$(pwd)",target="/mnt/host" dhardestylewis/taudem:tacc bash taudem_commands.sh

where taudem_commands.sh is written according to this template:

#!/bin/bash
pitremove -z /mnt/host/DEM.tif -fel /mnt/host/DEMfel.tif

Singularity instructions.

The Singularity pull command is similar to the Docker pull command:

singularity pull \
    --name taudem.sif \
    docker://dhardestylewis/taudem_docker:tacc

Once pulled, a one-off TauDEM command using Singularity can be issued:

singularity exec \
    taudem.sif \
    bash -c "pitremove -z /mnt/host/DEM.tif -fel /mnt/host/DEMfel.tif"

An interactive shell in the Singularity container may be used for troubleshooting or debugging:

singularity exec \
    taudem.sif \
    bash

TauDEM combined with other commands in a shell script

TauDEM may be wrapped in a shell script and run using Docker:

docker run \
    --name taudem_bash \
    --rm \
    -i \
    -t \
    --mount type=bind,source="$(pwd)",target="/mnt/host" \
    dhardestylewis/taudem_docker:tacc \
    bash -c './taudem_commands.sh'

where the file taudem_commands.sh may be written as:

#!/bin/bash

## Execute TauDEM
pitremove -z /mnt/host/DEM.tif -fel /mnt/host/DEMfel.tif 

To do the same using Singularity, execute:

singularity exec \
    taudem.sif \
    bash -c './taudem_commands.sh'

where taudem_commands.sh is written as above.