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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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Failed to download forest somatic.v0.7.4.forest.gz #259

Closed Axze-rgb closed 10 months ago

Axze-rgb commented 1 year ago

Hello,

the title is pretty self-explanatory. The command

/install.py --dependencies --forests failed.

Is there an issue with the cloud storage, such as it has moved, is not paid for any more, etc?

Thanks!

EDIT2: seems to be a billing issue on the Google cloud

dancooke commented 11 months ago

Hi, Sorry it's taken so long to address this - there was a billing problem with my Google Cloud account. I'll look to move the files over to Zenodo as suggested in #261 asap.

gambalab commented 11 months ago

An other free solution were you can put useful files is figshare or github with LFS (max file dimension is 2GB with the free plan)

Axze-rgb commented 11 months ago

Tanks Dan for taking the time to fix this. Octopus is an awesome tool! we need it.

Axze-rgb commented 11 months ago

Hello

do you have an idea about when this will be fixed? If I (and the community) can help, please let us know. Octopus is an awesome SNP callers, we must preserve it! Thank you

dancooke commented 10 months ago

I've added the forest files to the repo with LFS.

Axze-rgb commented 9 months ago

is it normal the files ends in .gz but are NOT compressed? Also, upon inspection they look like HTML files but I don't see where are the decisions. I am no expert though, but could you kindly double check you haven't uploaded the wrong file? Which would explain while all my call returns empty vcf. Thanks

jelber2 commented 9 months ago

I think maybe you are trying to download the pointers to the files as they were uploaded with git lfs.

As far as I know, you need to do the following, but note the error message at the bottom

git clone https://github.com/luntergroup/octopus
cd octopus/
# you need to install git-lfs
git lfs pull

batch response: This repository is over its data quota. Account responsible for LFS bandwidth should purchase more data packs to restore access.                                               
Failed to fetch some objects from 'https://github.com/luntergroup/octopus.git/info/lfs'

So, nothing more can be done until the data quota is increased or perhaps refreshes (not sure if it is a monthly thing?)

Axze-rgb commented 9 months ago

Oh, ok, thanks, so we still don't have the forest files available.

git lfs pull returns nothing for me

EDIT: ok for an unknown reason I had to redownload the repo. And I have the same error message as you.

@dancooke Is there a way we can help you? Maybe Zenodo can be a solution? https://zenodo.org/ (I am not involved with zenodo I have no conflict of interest).