How to download the database?

[jolespin]

The link to the download instructions brought me back to this for a full circle. Is there any way I can just use wget instead of installing software to download the data? Do you guys have the 4 GB dataset on Google Drive or any FTP site?

[simroux]

If not through Cyverse, the easiest way to download the database is probably via using the Docker version of VirSorter (https://github.com/simroux/VirSorter#docker---from-dockerhub). Otherwise, if neither of these solutions are working, you can also grab the tar.gz from google drive: https://drive.google.com/file/d/0B6Tg-jjiojemNF9vMEFfYkl5S2s/view?usp=sharing.

Best,

Simon

[jolespin]

That Google Drive link is exactly what I was looking for! Thank you! Looking forward to using your tool. I have this weird draft genome bin that looks viral from some of the annotations.

[simroux]

Sounds good, let me know if you have any issue or any question (always looking out for weird new viruses :-) )

[jolespin]

Quick question, when running:

Where are the virsorter-run files? I got docker install and want to deploy the image. Thanks!

docker run -v /Applications/VirSorter/virsorter-data:/data -v /host/path/to/virsorter-run:/wdir -w /wdir --rm discoenv/virsorter:v1.0.3 --db 2 --fna /wdir/Input_contigs.fna

[simroux]

I did not manage the docker part so not 100% sure, but my feeling was that you don't have to put any file in host/path/to/virsorter-run, this is just a path to a folder you'll create on your machine (that you can change however you want) for VirSorter to work in.

[wfgui]

If not through Cyverse, the easiest way to download the database is probably via using the Docker version of VirSorter (https://github.com/simroux/VirSorter#docker---from-dockerhub). Otherwise, if neither of these solutions are working, you can also grab the tar.gz from google drive: https://drive.google.com/file/d/0B6Tg-jjiojemNF9vMEFfYkl5S2s/view?usp=sharing.

Best,

Simon

If not through Cyverse, the easiest way to download the database is probably via using the Docker version of VirSorter (https://github.com/simroux/VirSorter#docker---from-dockerhub). Otherwise, if neither of these solutions are working, you can also grab the tar.gz from google drive: https://drive.google.com/file/d/0B6Tg-jjiojemNF9vMEFfYkl5S2s/view?usp=sharing.

Best,

Simon

The link seems to have expired,could you provide it again ？Thank you.

[simroux]

The database is now available via wget: wget https://zenodo.org/record/1168727/files/virsorter-data-v2.tar.gz

[JiqiuWu]

Hi Simon,

Have you updated the database? How many PCs are included in the database now?

Many thanks, Jiqiu

[simroux]

No update of the database recently, mostly because we have been working on VirSorter 2 :-) https://github.com/jiarong/VirSorter2

[JiqiuWu]

No update of the database recently, mostly because we have been working on VirSorter 2 :-) https://github.com/jiarong/VirSorter2

WOOOW! COOL! But if we use this tool, how to cite it?

Many thanks, Jiqiu

[simroux]

The paper should be on bioRxiv relatively soon, but in the meantime you can provide the link to the github repo.