Modifying Existing Containers

First off, it is important that modifying existing containers should only be done to avoid having to rebuild a container from scratch while optimizing the recipe file. The ultimate goal is for the container to be fully reproducible from the recipe file. However, there are some containers that can take 2 hours to build and if you forgot to add a folder to the PATH directory or other similarly simple mistakes, 2 hours is a long time to wait to verify the container is working properly.

With that said, this is how you can take a squashed non-writable container and create a writable version that you can modify.

sudo singularity build --writable utilities2.simg utilities.simg

In my case, I had installed many programs but they were not in the PATH so the container while had these programs installed didn’t know where to find them! The solution was to load modules in the shell or add the modules to the environment section of the recipe file.

sudo singularity shell --writable utilities2.simg
for d in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/*/bin; do export PATH="$PATH:$d"; done

Unfortunately, doing this in a writable image did not provide the desired result

Modifying Environmental variables that were set up in the recipe file

Going into a writable image and changing an environmental variable on the command line will not create a permanent change in the environmental variable. Changes you make will be lost the next time the container is used unless you modify the /environment file within the image. Below is an example of the /environment file from snpphylo prior to modifying the PATH variable.

Method 1

You can modify/update each section individually

sudo singularity build --writable snpphylo3.simg snpphylo.simg
sudo singularity build --section environment snpphylo3.simg ../recipe

More information can be found on the singularity wiki

Method 2

You can also modify/install/update from within a container. For the environment, it is easier to do method 1 above.

more /environment
# Custom environment shell code should follow

source /etc/profile.d/
source $SPACK_ROOT/share/spack/
export PATH=$SPACK_ROOT/isugif/snpphylo/bin:$PATH

More information about this can be found in this singularity issue

Building over an existing image.

If you change something in a recipe you can just re-execute the build command and it will build only the changes you made in the recipe file.

sudo singularity build container.simg recipe

Once you have made all the changes and your image is working the way you want then you can make those changes in your original recipe file and recreate it from scratch for full reproducibility.

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