PROBLEM SOLVING

This file outlines problems that users have faced and solved. Please contribute more by editing this document or raising a github issue. We cannot cover everything here of course and assume a basic understanding.

conda build environment fails

This is rare but it is possible that one of the softwares in the env.yaml file will fail to install. This is an issue with conda not Tapirs, try installing the program in question at the command line with conda -c conda-forge install PROGRAM. It might help to try a different repository such as -c bioconda instead of conda-forge. It might be worth googling "conda PROGRAM" just to see how Anaconda Cloud page suggests installing.

PROGRAM not found

Please check that you are in the correct conda environment. conda activate tapirs should make sure that you are in the tapirs environment. This could also be an error associated with failing to completely build the environment. You could try to update it using conda env update -f workflow/envs/env.yaml or just manually install the missing program with conda install -c conda-forge XXX

error involving cores

Some hosts require you to specify the number of cores on which to run your job. You can just modify your snakemake command to include --use-cores 8 although you can vary this number to suit your machine.

I really want to speed up the first run building the environments

We recommend using mamba not conda to build environments. Snakemake fully supports mamba. It is a LOT faster.