inst/RNA_git/git-lfs-howto.md

In amcdavid/GeneseeBulk: Pipeline, analysis functions and markdown templates for bulk RNAseq

Git LFS tips

Rstudio server doesn't use git lfs properly. Some third-party GUIs for git seem to support it, such as smartgit, or gitkracken. (I can't specifically endorse either though).

Workarounds to using LFS while staging in rstudio.

1. Open a terminal via ssh or the rstudio in the project directory and make sure git and git-lfs are loaded:

   module load git/2.30.1 git-lfs/2.13.2
   eval `ssh-agent`; ssh-add #optional, so you don't have retype your password constantly
   

   1. Stage / unstage files as normal in rstudio.

   2. Re-add the files (needed because lfs does something magical when git add is called). In your terminal:

      git add --renormalize . 3. Check that git lfs is tracking properly.

      git lfs status For the lfs files it should appear in this list and have LFS: <hashcode> next to the filename. If not, make sure it's being tracked with git lfs track <path/to/file.ext>, and then rerun step 2. 4. git commit 5. git push

Uhoh, something is broken:

1. I see "File should be pointer" message when I pull. This means that a file was added to the main repo rather than lfs. We can fix this going forward by calling:

   git lfs migrate import --no-rewrite <pathspec>
   

amcdavid/GeneseeBulk documentation built on March 26, 2022, 4:58 a.m.