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bonsai-team / matam

Mapping-Assisted Targeted-Assembly for Metagenomics
GNU Affero General Public License v3.0
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install matam on HPC without sudo permissions #64

Closed quetjaune closed 5 years ago

quetjaune commented 5 years ago

First, thank you for MATAM, i find it very useful.

I was trying to install it through conda in HPC but when running matam_assembly.py, get "No valid binary found for classifier". I could not find what is the issue here. Conda is the best option to install in HPC? Any suggestion are welcome

loic-couderc commented 5 years ago

Hi @quetjaune,

Conda is the recommended way of installing MATAM, even on HPC infrastructure.

From your error message, i can say that the classifier binary is not in your PATH. This binary come along with the installation of RDP -- rdptools conda package.

Maybe an error occurred during the installation. Are you sure that the installation process ended well?

An option would be to re-install this package:

conda install -c bioconda rdptools

Then, to check the installation, run the following command in your terminal: classifier If all went well, something like this will be printed out:

USAGE: ClassifierMain <subcommand args ...> default command is classify classify - classify one or multiple samples crossvalidate - cross validate accuracy testing ....

quetjaune commented 5 years ago

Hi @loic-couderc , Is working right now!! Thank you so much for your help.