Opfvta
This is a yoda-style[TODO cite] repository that contains all of the
code, data, configuration, and prose to generate an article replicating
the [TODO original cite].
How to clone this repository
This repository (and all yoda-style repos) contain.
submodules/subdatasets.
datalad install -r https://github.com/con/opfvta-replication-2023.git
cd opfvta-replication-2023
Some of the subdatasets/submodules are git-annex enabled, which means
that we can use datalad to retrieve the files (which are just
references, no "bits").
TMP: Add smaug remote (need access):
SshConfig
Host smaug smaug.dartmouth.edu
Hostname smaug.dartmouth.edu
AddKeysToAgent yes
port 11110
user <username>
git remote add smaug smaug:/mnt/btrfs/datasets/incoming/con/opfvta-replication-2023.git
datalad get . -s smaug
git remote add gin https://gin.g-node.org/TheChymera/mouse-brain-templates
datalad get . -s gin
Run datalad get . for each git-annex enabled repository below:
- /opfvta-replication-2023/code/opfvta
- /opfvta-replication-2023/inputs/opfvta_bidsdata
How to build and use the images
Analysis image
This container executes all parts of the original work:
- preprocessing
- analysis
- data visualization rendering
- latex rendering into original article with updated data
Configure the variables at the top of the root level makefile (provided
values are what we used). Then the OCI image can be built with:
make oci-build
The OCI container can be run with the following command.
We require the scratch directory to be explicitly specified, as it will end up containing large amounts of data (in excess of 200 GB), and any default might accidentally clutter a difficult to locate directory.
OPFVTA_SCRATCH_DIR="/your/cache/dir" make oci-run
The container image can be pushed to a container registry:
make push
You may need to build a singularity/apptainer image with the following
command:
make apptainer-build
After the apptainer image is built, it will need to be committed and the
new bits pushed to a git annex enabled repository.
LaTeX builder image
This container renders the LaTeX for the replication paper. The image is
blang/latex with some extra dependencies.
make build-latex
The paper can be rendered into a pdf with:
cd paper/source/
make article
Yaroslav Halchenko