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Aug 29, 2022
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Add instruction for working from a fork #129

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Add instruction for working from a fork
mguaypaq Aug 17, 2022
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Incorporate suggestions from review
mguaypaq Aug 29, 2022
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32 changes: 32 additions & 0 deletions README.md
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Expand Up @@ -51,6 +51,38 @@ git pull && git annex get .

See more at [the official documentation](https://git-annex.branchable.com/walkthrough/) and take note of our [in-lab troubleshooting](https://github.com/neuropoly/data-management/blob/master/git-annex.md).

## Working from a forked repository

> ⚠️ For advanced users only. Normally the instructions under [Download](#Download) should be enough.

If you have forked this repository on Github (so that you have a copy `your-user-name/data-multi-subject` of `spine-generic/data-multi-subject`), you will need to take a few extra synchronization steps to get the latest data with `git annex get`. Otherwise, you may get an error message like:
```
get some-file-name.nii.gz (not available)
No other repository is known to contain the file.

(Note that these git remotes have annex-ignore set: origin)
failed
```

1. In your local clone of `your-user-name/data-multi-subject`, make sure that `spine-generic/data-multi-subject` is also configured as a remote:
```
git remote -v
# the answer should show both your-user-name/data-multi-subject.git (probably named "origin")
# and spine-generic/data-multi-subject (probably named "upstream")
```

If `spine-generic/data-multi-subject` is missing, you can add it with:
```
git remote add upstream https://github.com/spine-generic/data-multi-subject.git
git config remote.upstream.annex-readonly true
```

2. Then, to update your local clone, make sure to fetch the `git-annex` branch from `spine-generic/data-multi-subject` before running `git annex get`:
```
git fetch upstream +refs/heads/git-annex:refs/remotes/upstream/git-annex
git pull && git annex get .
```

## Analysis

The instructions to process this dataset are available in the [spine-generic documentation](https://spine-generic.readthedocs.io/en/latest/analysis-pipeline.html).
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