Commit 0195f731 authored by Jeroen F.J. Laros's avatar Jeroen F.J. Laros
Browse files

Added documentation.

parent 44fdc324
# Project skeleton
A skeleton Git repository for analysis projects.
# Preparations
Install dependencies.
```bash
pip install cookiecutter
pip install python-gitlab
```
Configure Cookiecutter by editing `.cookiecutterrc` in your home directory.
```yml
---
default_context:
full_name: Your Name
email: UserName@lumc.nl
cookiecutters_dir: /path/to/cookiecutters/
```
Configure Python GitLab by editing `.python-gitlab.cfg` in your home directory.
```INI
[global]
default = gitlab
ssl_verify = true
timeout = 5
[gitlab]
url = https://git.lumc.nl
private_token = your_token_here
```
# Starting a project
To start a new analysis project based on this skeleton, follow the following
steps:
```bash
cookiecutter https://git.lumc.nl/sasc/cookiecutter-data-analysis.git
```
## Working together on the same clone
If you need to work with other people on the same repository clone on the Shark cluster, you can use the following command to give group access:
```bash
find -type d -exec chmod 775 {} \;
find -type f -exec chmod 664 {} \;
```
## Cloning to a portable disk (NTFS)
Presuming your disk is attached to your own computer and the repository is on
the Shark cluster, you can use the following commands.
git clone ssh://shark/path/to/project/my-project
cd my-project
For some reason `annex-ignore` is set to `true`, we need to set it to `false`.
git config remote.origin.annex-ignore false
Set the repository to *direct mode* to prevent making symlinks, otherwise it
will be very difficult for windows users to access the files.
git annex direct
SSH caching seems to be broken on NTFS.
git config annex.ssh-options "-S /tmp/ssh_mux_%h_%p_%r"
Or alternatively, disable SSH caching all together (slow when working with a
large number of files).
git config annex.sshcaching false
Get the content.
git annex get .
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