Singularity image for GLASS workflows

18-Nov-2017
v1.1.2s2

Build details for glass-consortium/glasstools images.

PS: Documentation to run workflows is not yet ready. Visit https://docker.glass-consortium.org for updates.

Current Build

See below on how to install Singularity version: 2.4-install_718360bb.g718360bb

singularity pull shub://glass-consortium/glasstools:beta

Automated build, when successfully built is available at Singularity Hub: https://www.singularity-hub.org/collections/262 with image tag: glass-consortium/glasstools:beta

• Download using Singularity, v2.4 or higher.
• Avoid running container as root. Singularity images does not require root privileges to run workflows.
• Default bind while running workflow is user ${HOME}.
• For better potability and disk mounts, ask your system admin to configure /etc/singularity/singularity.conf and set enable overlay = yes. Read http://singularity.lbl.gov/docs-mount for details.

Manual build

We recommend pulling pre-built Singularity image from Singularity registry at https://www.singularity-hub.org/collections/262

Manual build is for improvement and debugging of current beta image, especially with reducing image size and adding shortcodes to additional GLASS workflows.

git clone https://github.com/glass-consortium/glasstools.git
cd build

singularity build glasstools_keystone_beta.simg Singularity.beta
singularity inspect glasstools_keystone_beta.simg

See file: glasstools_keystone_beta.simg.inspect.log for image details.

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How to install Singularity

• One time installation, requires admin privileges

Please ask your system administrator to install Singularity with following version. While installation should be done by IT administrator, running GLASS workflows does not require sudo privilege. Also, unlike potential root escalation while running docker container, Singularity based workflows are more isolated from host environment and less vulnerable to root escalation. Visit http://singularity.lbl.gov/user-guide#security-and-privilege-escalation for more on security.

• GLASS workflows are using Singularity v2.4

Full version at the time of install: v2.4-install_718360bb.g718360bb
Commit: https://github.com/singularityware/singularity/commit/718360bb20b66cbafb85dd9d0a73bd6bb60c7a1f

• For better compatibility with pre-built GLASS image, please install Singularity from forked reposioty as follows:

umask 0022

git clone https://github.com/glass-consortium/singularity.git
cd singularity

## confirm last commit ID to be 718360bb20b66cbafb85dd9d0a73bd6bb60c7a1f for HEAD -> master branch
git log --name-status HEAD^..HEAD

## fork master branch to a new branch, named install_718360bb
git checkout -b install_718360bb
git status

This will show...

On branch install_718360bb
nothing to commit, working tree clean

./autogen.sh && ./configure --prefix=/usr/local && make

# return exit code for compilation status
echo $?

## only one time, we need root privileges
sudo make install

## return to non-root user environment
sudo -k

cd ${HOME} # non-root user

singularity --version

This will show 2.4-install_718360bb.g718360bb. If so, installation is identical to an environment used to build GLASS Singularity image.

Bugs, issues

Report issues related to setting up Docker/Singularity image and running workflows at https://github.com/glass-consortium/glassdocs/issues.

Credits

• Original Singularity file was based on https://github.com/jekriske/r-base by Jeff Kriske