![]() ![]() ![]() Git-annex metadata mri_convert/ -s fstags+=makeinstall Git-annex metadata mri_convert/ -s fstags=makecheck When adding metadata to an annex file, it is best to start with a clean checkout of the repository and be in the 'dev' branch. ![]() Git-annex metadata mri_convert/Īssigning metadata to a datafile is the job of a source code administrator, similar to adding a datafile. To show all the metadata associated with a file: Git-annex get -metadata fstags=makeinstall. To get only the data files required for installation: It is essential that data files get tagged properly so that our servers and diskspace are not overwhelmed when only a known subset of the data is required. The data files have been broken down into the following 2 categories:įiles required for build time checks - makecheckįiles required for a local installation - makeinstall Freesurfer utilizes tags so that subsets of the data can be retrieved without having to download everything. Git -annex provides the ability to tag data files. Then, after making modifications, re-add it to the annex: To modify the contents of a data file, first unlock it, which eliminates the symlink: Or to retrieve everything under the current directory: Then, to retrieve the contents of a data file: This must be done every time you want to download new annex data: Git commit -m "added test to subdirectory"įirst, fetch the state of the remote data source. NOTE: Please make sure the file you are adding has group-writable and world-readable permissions otherwise, people will not be able to pull your new file from the server.Ĭhmod 664 # optional - just make sure it's world readable The following example assumes we want to add an example test script and test data tarball called '' to a subdirectory. Generally, only the freesurfer source code administrators should add a file to the annex - especially since only users at the Martinos Center will have write access to the filesystem. Git remote add datasrc file:///space/freesurfer/repo/annex.gitįor those developing outside of Martinos, run:Īfterwards, the output of git remote -v should look something like this:ĭatasrc file:///space/freesurfer/repo/annex.git (fetch)ĭatasrc file:///space/freesurfer/repo/annex.git (push) For those developing on the Martinos filesystem, cd into your repository and run: Instructions to do this are described below.Īs described in the build guide, the annex data source must be setup as a remote repository. It's broken because you have yet to pull the actual data files from the separate annex repository in /space/freesurfer/repo/annex.git. For example, if you were to create a fresh clone of the freesurfer repository from github, you would see that mri_convert/ is actually a broken relative symlink to a hashed file in the. When you commit a new data file with git annex, the main repo is aware of this new file, but it will actually store it as a symlink. Git annex is a tool for storing large files outside of the main repository. Additional documentation can be found on the git-annex website. For basic instructions on retrieving annex data, visit the build guide. This page details how to work with git-annex, the software used for storing and retrieving these data files in the freesurfer git repo, and it's mostly meant as a guide for internal maintainers. Think of source code as text files, and think of data files as binary files not required for compilation. Instead, they should be stored in a separate space, reserved for times when retrieval is required, like for updating test data, performing local installations, etc. ![]() The freesurfer repository contains many large binary files that can't be stored directly on github. Please refer to this site/make edits here for the most updated information: ![]()
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