search

replikation / What_the_Phage

WtP: Phage identification via nextflow and docker or singularity
https://mult1fractal.github.io/wtp-documentation/
GNU General Public License v3.0
103 stars 15 forks source link

How to get the version of tools that What the Phage used？ e.g. virsorter，virfinder etc. #141

Closed marineLZ closed 2 months ago

marineLZ commented 3 years ago

Sometimes， we want to know the version number of built-in tools

mult1fractal commented 3 years ago

Hey below you can find the current versions of the phage identification tools we use. We are currently working on a complete overhaul of wtp. Thanks for the suggestion. we will include all tool versions in a final report overview 👍🏽

VirFinder v1.1 PPR-Meta v1.1 VirSorter v1.0.6 (with and without virome mode) DeepVirFinder v1.0 Metaphinder with no release version (using default database and own database) MARVEL v0.2 sourmash v2.0.1 Vibrant v1.2.1 (with and without virome mode) VirNet v0.1 (21) phigaro v2.3.0 seeker no release version

marineLZ commented 3 years ago

Got it. Thanks for your prompt reply and excellent work.

replikation commented 3 years ago

we tag the container /tool used with their version number, see here. However some don't have a version number as pointed out by @mult1fractal

marineLZ commented 3 years ago

I see in this file that : multifractal/vibrant:0.5 multifractal/virfinder:0.2

As the lattest versions are Vibrant v1.2.1 and VirFinder v1.1, does this two version number matched?

mult1fractal commented 3 years ago

no... the tags behind the containers are from my first coding adventures... I will also update them to match the actually used version

-->use the list from my previous comments these are the correct versions WTP uses atm.

deminatanja commented 1 year ago

Hi @mult1fractal , I used the tool in Feb 2023, were the versions still same at that time point? I am only interested in Virsorter2, PPR-Meta and DeepVirFinder. Best, Tatiana

mult1fractal commented 1 year ago

Hey

VirSorter 2.2 PPR meta has no version (has no help function where I can read out the version) deepvirfinder v1.0

If you want to check yourself you can check the link: https://github.com/replikation/What_the_Phage/blob/master/configs/container.config

and access in your terminal the docker like this: docker run --rm -it -v $PWD:/input papanikos/virsorter-2:2.2.1--fa935f8 then use the corresponding tool name: e.g. virsorter -h and check the tool version

I did not updated the tools yet.. but thats a good idea to do... I hope it wont break anything :D

deminatanja commented 1 year ago

Thanks a lot! :)