Re: VIP

[Tony Travis <tony.travis@minke-informatics.co.uk>]

On 08/07/2020 18:01, Tony Travis wrote:
> On 08/07/2020 14:56, Michael Crusoe wrote:
> > [...]
> > Perhaps try the author's vip2 container? 
> > https://hub.docker.com/r/yang4li/vip2 Though I can find no source for 
> > either container, so it is a bit risky.
>
> Hi, Michael.
>
> OK, I've pulled the vip2 container and I'm having a look at it now...
>
> Interestingly it uses "miniconda3" under Ubuntu 18.04, which is how I 
> have been running it without a Docker container. However, there is no 
> documentation about how to build the necessary databases.

Hi, Michael.

The VIP2 container has a binary in it to replace the VIP.sh script, but 
no source code and no information about how to create the databases it 
requires. Unlike the VIP-0.2.0 container on GitHub there are no 
pre-existing databases we can use in the VIP2 container.

I've had partial success running VIP-0.2.0, which I extracted from the 
docker image and created a Bioconda env: The GitHub repo only contains 
VIP-0.1.1, which has been cloned and modified to create VIP-0.2.0 in the 
docker image, but these changes have not been committed and pushed back 
into the GitHub repo. The VIP project appears to have been abandoned...

Only three of six jobs I started over a week ago have finished and I'm 
looking for an alternative virus identification pipeline that can do the 
analysis better/faster.

The VIP2 container appears to run "Centrifuge", so I was interested to 
see the messages about "Centrifuge" here and I would welcome help/advice 
from anyone who has used "Centrifuge" to detect viruses in a microbiome.

Thanks,

  Tony.

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