Using the CTF tools with a Singularity Container
The current version of the CTF tools run under CentOS (Linux) version 6.9. To support the MEG user community, we have a Singularity container for CentOS 6.9 containing the necessary libraries to run them. This allows MEG users to run the tools under the operating system (Windows, Mac OSX, Linux) of their choice.
Singularity is a Operating-system-level virtualization solution where an operating system can host another operating system in an isolated container. To run a Singularity container on your operating system, you need to install the Singularity software for your operating system. There are install packages for the major operating systems from the Singularity website.
- Singularity container running CentOS 6.9 with the CTF tools
- Singularity container ctf-6.1-sing.tar download
Example usage: singularity shell --bind /data:/mnt/data ctf6.1.sif where the /data file system holds your CTF data set and mounts under /mnt/data inside the container (your /home directory and the /tmp file systems are automatically visible inside the container)
Note that the ctf6.1.sif file is inside the .tar file.
Another way to use the Singularity container is to use a wrapper script. This allows you to run CTF commands from outside the Singularity environment.
To do this, unpack the .tar file above, and run the mkwrappers script.
mkdir tmp cd tmp tar -xf /path/to/ctf-6.1-sing.tar ./mkwrappers
You don't need the tmp directory after that. The wrappers are installed in /usr/local/ctf/bin, so put that in your path.
- biowulf.nih.gov users
- module load ctf
The ctf container is already installed on biowulf.
- General use
For other machines, use the following bash script to shell into the singularity container.
#!/bin/bash # goctf.sh singularity shell --bind /data/username:/mnt/data ctf6.1.sif killall -s msgd 2>/dev/null
DataEditor and the other CTF tools communicate with each other using the msgd service, which will automatically be launched if it isn't already running. This service is not killed when you exit from the singularity container, so you will end up with a persistent process. To prevent this from occurring, just kill it, as above.
You may want to add this stanza to your ~/.bashrc file. This sets both the command prompt and the command history format for your shell inside the container
if [ ! -z "$SINGULARITY_CONTAINER" ]; then ## PS1 is set inside the container HISTFILE=~/.bash_history HISTTIMEFORMAT='%Y%m%d/%H:%M:%S ' else export PS1='[\h \w]$ ' fi