This page describes how to deal with adding and tagging data files in the freesurfer source code repository.
Initial Setup
Based in the information included in the Freesurfer_github page, the remotes of your freesurfer repo working directory should look something like:
git remote -v datasrc file:///space/freesurfer/repo/annex.git (fetch) datasrc file:///space/freesurfer/repo/annex.git (push) origin git@github.com:zkaufman/freesurfer.git (fetch) origin git@github.com:zkaufman/freesurfer.git (push) upstream git@github.com:freesurfer/freesurfer.git (fetch) upstream git@github.com:freesurfer/freesurfer.git (push)
Adding a data file
The following example assumes we want to add a data file called 'testdata.tar.gz' to the 'distribution' directory:
Getting a data file
To retrieve the contents of a data file:
## Retrieve a specific file git annex get mri_em_register/testdata.tar.gz ## Retrieve everything under the current directory (not recommended) git annex get .
To retrieve everything (not recommended):
== Tagging a data file ==
The data files have been broken down into the following 3 categories, and it is essential that data files get the proper tag(s) so that our servers and diskspace is not overwhelmed when only a known subset of the data is required.:
1. Those being required for build time checks (tagged '''makecheck''')
1. Those required for a local installation (tagged '''makeinstall''')
1. Everything else (untagged)
=== Display metadata ===
To show all the metadata associated with a file:
{{{
git annex metadata mri_em_register/testdata.tar.gz
Assign metadata
To assign a tag to an existing datafile.
git annex metadata mri_em_register/testdata.tar.gz -s fstags=makecheck git annex sync
We can also append tags:
git annex metadata mri_em_register/testdata.tar.gz -s fstags+=makeinstall
To list all files with a given tag:
git annex find --metadata fstags=makecheck
To download all datafiles with a given tag:
## Get only the data files required for build time checks (1.9 GB) git annex get --metadata fstags=makecheck . ## Get only the data files required for local installation (4.3 GB) git annex get --metadata fstags=makeinstall . ## Just give me everything! Not Recommended (6.8 GB) git annex get .