Running LTRpred docker container in userspace with udocker

[ibebio]

The LTRpred docker container can be run on systems where docker is not available and root privileges are not an option via udocker. Udocker is written in Python and can be installed via pip. The following sequence of commands starts up the LTRpred container in user space:

# Create and activate conda environment, optional
conda create -n udocker_prod -c defaults python=2.7
conda activate udocker_prod

# Install most recent version from udocker github repo
pip install git+https://github.com/indigo-dc/udocker

# Prepare container
udocker pull drostlab/ltrpred
udocker create --name=ltrpred drostlab/ltrpred

# Required on some systems to run the container
export PROOT_NO_SECCOMP=1

# Run container
udocker run ltrpred

[HajkD]

Dear Ilja,

Thank you so much for this absolutely brilliant suggestion!

This will help a lot of users to run the LTRpred Docker container in a Conda environment and doesn't require a conversion to Singularity containers.

Many thanks,
Hajk

[123jjhy]

Hi,
Ask if this method also necessarily requires root permissions?

[HajkD]

Not when it is converted to a Singularity Container.

[123jjhy]

What is a Singularity Container？ I am a green hands，could you give me some more Pointers？

[HajkD]

https://docs.sylabs.io/guides/3.5/user-guide/introduction.html

[123jjhy]

OK. Thank you.