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INSTALL.md

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Installation and set up

In order to set up these resources, some software may be required

Conda environment (optional)

The above and other miscellaneous dependencies may be installed in a Conda environment using the provided environment.yml file as (conda may be replaced by mamba executable):

conda env create -f environment.yml  # create cosgap environment
conda activate cosgap
# do this and that...
conda deactivate

Clone the repository

To download all files of the last revision of this project, issue:

cd path/to/repositories
git clone --depth 1 https://github.com/comorment/containers.git
cd containers
git lfs pull  # pull "large" files

Update the Singularity Image Files (containers)

We are presently migrating container builds as distributed here to the GitHub Container Registry. Current and future image build artifacts (Singularity and Docker) are listed under Packages.

To obtain updated versions of the Singularity Image Format (.sif) container files provided here, issue:

cd path/to/repositories/containers/singularity
mv <image>.sif <image>.sif.old  # optional, just rename the old(er) file
apptainer pull docker://ghcr.io/comorment/<image>:<tag>  # or
singularity pull docker://ghcr.io/comorment/<image>:<tag> # or 
oras pull ghcr.io/comorment/<image>_sif:<tag>  # note the "_sif" suffix

where <image> corresponds to one of {hello|gwas|python3|r} and <tag> corresponds to a tag listed under https://github.com/comorment/containers/pkgs/container/<image>, such as latest, main, or sha_<GIT_SHA>. The oras pull statement pulls the <image>.sif file from https://github.com/comorment/containers/pkgs/container/<image>_sif using the ORAS registry, without the need to build the container locally.

Pulling and using Docker image

To pull the corresponding Docker image, issue:

docker pull ghcr.io/comorment/<image>:<tag>

If working on recent Macs, add the --platform=linux/amd64 flag after docker pull. This may allow replacing singularity exec ... or apptainer exec ... statements with appropriate docker run ... statements on systems where Singularity or Apptainer is unavailable. Functionally, the Docker image is equivalent to the Singularity container, but note that syntax for mounting volumes and invoking commands may differ. Please refer to docs.docker.com for more information.

Note

Note that the provided Docker image may not support all CPUs, and may not be able to run on all systems via CPU virtualization. An option may be to build the Docker image on the host machine directly (e.g., M1/M2/M3 Macs, PCs with older Intel CPUs), as:

docker build --platform=linux/amd64 -t ghcr.io/comorment/<image> -f dockerfiles/<image>/Dockerfile .

A minimal usage example may be to invoke the PLINK tool and its help function in the hello container:

export HELLO="ghcr.io/comorment/hello:latest"
export PLINK1="docker run --platform=linux/amd64 --rm -v ${HELLO}/usecases:/home -v ${HELLO}/reference:/REF -w/home --entrypoint=plink1 ${HELLO}"
$PLINK1 --help

A more complete example is provided for MiXeR here.

Systems without internet access

Some secure platforms do not have direct internet access, hence we recommend cloning/pulling all required files on a machine with internet access as explained above and archiving the containers directory with all files and moving it using whatever file uploader is available for the platform.

cd /path/to/containers
SHA=$(git rev-parse --short HEAD)
cd ..
tar --exclude=".git/*" -cvf containers_$SHA.tar containers

Install (old)

We recommend to clone this entire repository using git clone --depth 1 https://github.com/comorment/containers.git. However, you need to install the Git LFS extension. This is done by downloading and unpacking the GitLFS package, adding git-lfs binary to a folder that is in your PATH, and running git lfs install command.

mkdir ~/bin
export PATH="/home/$USER/bin:$PATH"        # good idea to put this in your ~/.bashrc or ~/.bash_profile
wget https://github.com/git-lfs/git-lfs/releases/download/v2.13.2/git-lfs-linux-amd64-v2.13.2.tar.gz
tar -xzvf git-lfs-linux-amd64-v2.13.2.tar.gz
cp git-lfs /home/$USER/bin
git lfs install

Now you're all set to clone this repository (note that adding --depth 1 to your command as shown below will limit the amount of data transferred from GitHub to your machine):

git clone --depth 1 https://github.com/comorment/containers.git

At this point you may want to run the following find&grep command to check that all git lfs files were downloaded successfully (i.e. you got an actual content of each file, and not just its git lfs reference). The command searches for and lists all files within $COMORMENT folder which contain a string like oid sha, likely indicating that git lfs file hasn't been downloaded. If the following commands doesn't find any files that you're good to go. Otherwise you may want to re-run your git clone commands or investigate why the're failing to download the actual file.

find $COMORMENT -type f -not -path '*/.*' -exec sh -c 'head -c 100 "{}" | if grep -H "oid sha"; then echo {}; fi ' \; | grep -v "oid sha256"

For TSD system, a read-only copy of $COMORMENT containers is maintained at these locations (please read github/README.md file before using these copies):

# for p33 project
export COMORMENT=/cluster/projects/p33/github/comorment

# for p697 project
export COMORMENT=/ess/p697/data/durable/s3-api/github/comorment

Once you have a clone of this repository on your system, you may proceed with docs/singularity/hello.md example. Take a look at the README file in the docs/singularity folder, as well as detailed use cases in usecases.

To simplify instructions throughout this repository we use certain variables (it's a good idea to include them in your .bashrc or similar):

  • $COMORMENT refers to a folder with comorment and reference subfolders, containing a clone of the containers and reference repositories from GitHub. Cloning reference repository is optional, and it's only needed for internal work within the CoMorMent project - for normal use you may proceed without it.
  • $SIF refers to $COMORMENT/containers/singularity folder, containing singulairty containers (the .sif files)
  • SINGULARITY_BIND="$COMORMENT/containers/reference:/REF:ro,$COMORMENT/reference:/REF2:ro" defines default bindings within container (/REF, /REF2). If you don't have access to private reference, try out commands without mapping $COMORMENT/reference:/REF2:ro - most (if not all) of the exmples don't require private reference data.
  • We assume that all containers run with --home $PWD:/home, mounting current folder mounted as /home within container
  • We also recommend using --contain argument to better isolate container from the environment in your host machine. If you choose not to mount --home $PWD:/home, you may want to add --no-home argument.
  • You can choose to exclude passing environment variables from the host into the container with the --cleanenv option. Read more about it here.