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RemiAllio / MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
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git clone is now up to speed with git-lfs clone #27

Closed sam217pa closed 2 years ago

sam217pa commented 2 years ago

Hi and thanks for MitoFinder!

Just wanted to let you know that I followed your instruction and got a warning message telling me that git clone now has comparable speed to git lfs clone (working with git 2.20.1, git lfs 1.5.2); that should make the installation instruction for singularity a bit simpler.

cheers,

RemiAllio commented 2 years ago

Hi !

Thank you for your feedback! I don't know if I can use git clone instead of git lfs clone since the size of the container is bigger than requested for git clone. That's why I use git lfs clone... However, I will soon upload the MitoFinder container to the singularity cluster to allow it to be downloaded directly with singularity. I think this should make the installation much easier.

Best, Rémi

sam217pa commented 2 years ago

Yes it will 👍

Do you know about https://biocontainers.pro/tools/mitofinder? They host both a docker and singularity image of mitofinder that seems to include dependencies as well (found megahit and metaspades.py, can't locate mitfi.jar though.).

I can try it out and let you know how it goes if that helps?

RemiAllio commented 2 years ago

Hi,

I had no idea about the container you mentioned. Do you know who created it? Do you think this biocontainer is used?

Here is the command to download the last singularity image of MitoFinder :-) singularity pull --arch amd64 library://remiallio/default/mitofinder:v1.4.1

I will update the readme in the github as soon as possible. Cheers, Rémi

sam217pa commented 2 years ago

Excellent 👍

I don't know who created it. From what I understand recipes pushed to bioconda (as is mitofinder https://anaconda.org/bioconda/mitofinder) are also deployed as containers thanks to the biocontainers continuous integration. The repo listed in the bioconda recipe is https://github.com/parklab/xTea though, which doesn't have anything to do with MitoFinder 🤔🤔 The biocontainer page say it was downloaded 565 times, so I guess it is used 👍

cheers!

sam217pa commented 2 years ago

Just wanted to let you know that the singularity image you pushed worked flawlessly on pre-computed assemblies on my side.

Nice work!

RemiAllio commented 2 years ago

Nice! Thank you :slightly_smiling_face:

Regarding your previous message: This is quite strange! It is indeed downloaded enough to assume that it is used even though I don't know if this container actually works... I'm not sure I understand the connection with https://github.com/parklab/xTea either. :thinking:

Anyway, thanks for pointing it out to me :slightly_smiling_face: