From 8bb8ac548ac70c6cdca9a87b55de0f120f1b721f Mon Sep 17 00:00:00 2001 From: Sergey Koren Date: Fri, 7 Jun 2024 11:12:08 -0400 Subject: [PATCH] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c7066be9..49a6923d 100644 --- a/README.md +++ b/README.md @@ -129,7 +129,7 @@ To run in PoreC mode, reads should be provided using the --porec option. For exa Hi-C/PoreC integration was tested mostly on human and primate genomes. Please see the --rdna-scaff-ref, --rdna-tangle, --uneven-depth and --haplo-divergence options if you want to assemble something distant from human and/or have uneven coverage. If you encounter issues or have questions about appropriate parameters, please open an [issue](https://github.com/marbl/verkko/issues). ### Running on a grid -By default, verkko will run the snakemake workflow and all compute on the local machine. Support for SGE, Slurm and LSF (untested) can be enabled with options `--sge`, `--slurm` and `--lsf`, respectively. This will run the snakemake workflow on the local machine but submit all compute to the grid. To launch the both the snakemake workflow and compute on the grid, wrap the verkko command in a shell script and submit using your scheduler. +By default, verkko will run the snakemake workflow and all compute on the local machine. Support for SGE, Slurm and LSF (untested) can be enabled with options `--sge`, `--slurm` and `--lsf`, respectively. This will run the snakemake workflow on the local machine but submit all compute to the grid. To launch the both the snakemake workflow and compute on the grid, wrap the verkko command in a shell script and submit using your scheduler. If you're using conda, you may need to make the conda-installed python your default. You can do this with the `--python` option when calling verkko For cluster runs verkko uses different cpu/memory/time options for different parts of the pipeline. Usually a user does not need to change them, however advanced tuning is possible with ---run options.