search

jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
346 stars 81 forks source link

Workflow, tool version outline #825

Open s-junguy opened 2 months ago

s-junguy commented 2 months ago

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

jtamames commented 2 months ago

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

s-junguy commented 2 months ago

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 commented 2 months ago

The versions of the tools are the same than the pipeline

s-junguy commented 2 months ago

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 commented 2 months ago

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 commented 2 months ago

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 commented 2 months ago

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