Workflow, tool version outline

[s-junguy]

Hi, is there a way I can get access to a list of tools and their version I ran within the pipeline?

[jtamames]

Hello
The list of all features is in the manual.
Version can be obtained with SqueezeMeta.pl -v (also in the manual)

[s-junguy]

Thanks for your help but I not only need the version from the pipeline but also the versions from every single tool that has been executed within the pipeline. If I click on the links under "18. License and third-party software", I only get to the github site.

[jtamames]

The versions of the tools are the same than the pipeline

[s-junguy]

If I execute SqueezeMeta.pl -v I only get

***
1.6.3, September 2023

but I also need the versions from every tool like trimmomatic, megahit etc. I still don't know where to find these versions...

[fpusan]

That's an oversight on our part, I don't think this is written anywhere explicitly You will have to check manually.

The /path/to/SqueezeMeta/scripts/SqueezeMeta_conf.pl has the location of the different tools used in SqueezeMeta (some we redistribute ourselves, some we obtain via conda). This should help you locating the different tools in order to get their version.

We definitely need to provide this information in a straightforward way, so I will leave this issue open until I write a fix.

[jtamames]

The tool list and URLs leading to tool's repos can be found in https://github.com/jtamames/SqueezeMeta#18-license-and-third-party-software

[fpusan]

Yeah but this doesn't include the actual versions that we are calling within SqueezeMeta. In most cases it is the latest version, but that can not be taken for granted