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
