Re: VIP

[Steffen Möller <steffen_moeller@gmx.de>]

Hi Tony,

On 25.08.20 01:09, Tony Travis wrote:
> 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.

https://tracker.debian.org/pkg/centrifuge

was only very recently added to the distribution. I _very_ much support
ourselves shifting our discussions from packaging towards using our
packages. @Tony, if you have any more or less public dataset in mind
that we all could work along with then this would possibly be helpful.

Best,

Steffen