Cloning Github repository - EBI-Metabolights/SAFERnmr GitHub Wiki
Intended for those who don't usually work with Github. These are intended to be super specific instructions because Github is super useful but also a little confusing to get started with.**
There are two ways you could do this:
-
Install Github Desktop. Set up Github through desktop. I have a
Github
directory in in myDocuments
folder, and usually mount my repositories there. -
In the Github Desktop App, you should see something like this in the top left corner:
show example
-
Click the Add button there
show example
-
Click 'Clone Repository'. Select
URL
:show example
</details>
show example
-
Use the 'Choose' option to set your mounting folder to
Documents/Github
, or wherever you want to mount your repos on your machine. Then, enter the URL of SAFER (https://github.com/EBI-Metabolights/SAFER
) into the field that saysURL or username/repository
, and you should see theLocal Path
field update. This means that Github Desktop will create a folder calledSAFER
in that location (e.g.Documents/Github
in my case). This is where all your other cloned repositories will live by default. In theSAFER
folder is where all the code for the package will go:show example
-
Click the
Clone
button, and you should see the following:show example
-
This means the files are being downloaded. Once that's done, you'll get this:
show example
-
The cool thing is, now Github Desktop will now update all of the files in the
SAFER
folder with the most recent release version whenever you open the app and click theFetch origin
button. Sometimes it will sayPull origin
. There are probably differences in what these mean, but either is fine for our purposes. -
Take note of where this repo is mounted. You can find this information by right-clicking the
Current Repository' button on the top left corner (where we started) and clicking
Reveal in Finder` (on a Mac):show example
which will open a Finder window in that location.
<details>
<summary>show example</summary>
<img width="725" alt="clone_reveal_2" src="https://github.com/EBI-Metabolights/SAFER/assets/15824301/8e0e8048-2763-4de4-9e68-97c95b28eeb3">
</details>
- On a Mac, you can then use
Cmd-Option-C
to copy the filepath of the folder (e.g./Users/mjudge/Documents/GitHub/SAFER
in my case). This will be useful for pipeline setup later on, and we'll refer to it aspath_to_SAFER_repo_clone
That's it! Feel free to get in touch if this doesn't work for you - and feel free to modify as you like, create forks, etc. if you want to develop off of what we've done.
(seriously, not recommended, but if you can't be bothered with Github, it's possible) Beware: you won't receive any updates to the code.
-
Go to the SAFER Github page.
-
Click the Green
Code
button, then selectDownload ZIP
:show example
-
(Move if you want) and Expand it locally:
show example
-
Copy the file location and use that as
path_to_SAFER_repo_clone
in the setup process
But, really: it's not the best option.