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GN1 github problem

When trying to push to github, a commit from 2018 is blocking:

tux01:~/genenetwork1$ git push
Enumerating objects: 41, done.
Counting objects: 100% (41/41), done.
Delta compression using up to 128 threads
Compressing objects: 100% (21/21), done.
Writing objects: 100% (23/23), 118.03 MiB | 23.15 MiB/s, done.
Total 23 (delta 20), reused 3 (delta 2)
remote: Resolving deltas: 100% (20/20), completed with 18 local objects.
remote: error: File web/images/upload/MouseTissuesRWWMay08.xls is 262.53 MB; this exceeds GitHub's file size limit of 100.00 MB
remote: error: GH001: Large files detected. You may want to try Git Large File Storage - https://git-lfs.github.com.
To github.com:genenetwork/genenetwork1.git
 ! [remote rejected] lily -> lily (pre-receive hook declined)
error: failed to push some refs to 'git@github.com:genenetwork/genenetwork1.git'

This is because of a resync of lily. I should not do that again.


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To solve this I have to remove the large file(s). Fortunately not many people are using genenetwork1 code base, so I can rewrite the git store.

find . -size +20M -exec ls -lh \{\} \;
-rwxr-xr-x 1 wrk wrk 263M Dec 15 15:38 ./web/images/upload/MouseTissuesRWWMay08.xls

Make a backup(!)

Remove a file (dir with rm -rf). Make sure you do it for open branches too

rm ./web/images/upload/MouseTissuesRWWMay08.xls
git filter-branch --tree-filter 'rm -f web/images/upload/MouseTissuesRWWMay08.xls' HEAD
git filter-branch --force --index-filter 'git rm --cached --ignore-unmatch \
  MouseTissuesRWWMay08.xls' --prune-empty --tag-name-filter cat -- --all
git reflog expire --expire=now --all && git gc --prune=now --aggressive

Note this rewrites git history. It is a dangerous command. Also, make sure all others do a fresh checkout of the repo.


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