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fakedrtom / SVAFotate

MIT License
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installation issue using pip #21

Closed prasundutta87 closed 10 months ago

prasundutta87 commented 10 months ago

Hi,

I tried installing SVAFotate in a new conda enviroment today and I got this error-

`pip install git+https://github.com/fakedrtom/SVAFotate.git Collecting git+https://github.com/fakedrtom/SVAFotate.git Cloning https://github.com/fakedrtom/SVAFotate.git to /tmp/pip-req-build-9akg5rr3 Running command git clone --quiet https://github.com/fakedrtom/SVAFotate.git /tmp/pip-req-build-9akg5rr3 Downloading supporting_data/gnomad.v4.bed.gz (356 MB) Error downloading object: supporting_data/gnomad.v4.bed.gz (b7ea0af): Smudge error: Error downloading supporting_data/gnomad.v4.bed.gz (b7ea0af44cfad1061397aadf2425d355c8a4b0052b51aeb23c9f5905fd15bf1f): batch response: This repository is over its data quota. Account responsible for LFS bandwidth should purchase more data packs to restore access.

Errors logged to /tmp/pip-req-build-9akg5rr3/.git/lfs/logs/20240129T171426.634724821.log Use git lfs logs last to view the log. error: external filter git-lfs smudge -- %f failed 2 error: external filter git-lfs smudge -- %f failed fatal: supporting_data/gnomad.v4.bed.gz: smudge filter lfs failed warning: Clone succeeded, but checkout failed. You can inspect what was checked out with 'git status' and retry the checkout with 'git checkout -f HEAD'

error: subprocess-exited-with-error

× git clone --quiet https://github.com/fakedrtom/SVAFotate.git /tmp/pip-req-build-9akg5rr3 did not run successfully. │ exit code: 128 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error

× git clone --quiet https://github.com/fakedrtom/SVAFotate.git /tmp/pip-req-build-9akg5rr3 did not run successfully. │ exit code: 128 ╰─> See above for output.`

Is some update going on, in the lines of gnomad.v4 as seen above in the error message?

Regards, Prasun

fakedrtom commented 10 months ago

Yes, there is a problem with the gnomad.v4.bed.gz file and it is no longer usable for the time being. I believe this is the reason for the problem. I have removed gnomad.v4.bed.gz from the repo for the time being. Would you mind trying again and seeing if the installation works now?

prasundutta87 commented 10 months ago

HI @fakedrtom..thanks for the quick reply. Yes, it worked now! Thanks a lot!

fakedrtom commented 10 months ago

Great! I'll hopefully have the new gnomAD back and in a more usable form soon.