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biologger / speciesprimer

The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.
GNU General Public License v3.0
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How to run without Doctor container? #28

Open MonicaSteffi opened 4 months ago

MonicaSteffi commented 4 months ago

Hi,

Is there any possibility to run SpeciesPrimer without docker container? Since I do not have admin rights, it is hard to install docker container

hatchhailey commented 4 months ago

I am also wondering this

Theoretically I think you should be able to as long as you have the right dependencies

My only problem is I can't seem to sort out how the paths should be set up for the script to be able to find everything it needs as if it were running in the container

biologger commented 3 months ago

Hi,

Sorry for the late reply.

As @hatchhailey stated it is possible in theory when all the dependencies are installed and all paths are added to the Unix PATH Variable. But it may be difficult to get the correct versions of all dependencies, as the tool is quite old now.

The easiest way would be to use docker, podman or a similar tool.

I will look into this issue and report back, but it may take a while as I do not have that much spare time right now.