paudano
commented
2 years ago See the README.md under "Running PAV". These are scripts you setup for your environment. For example, if you need to load modules with software tools, like minimap2, then that would go into the script followed by the Snakemake command to submit jobs (or run on a single machine). There are example scripts in comments at the bottom of rundist and runlocal in the root of the PAV repository.
If you need to distribute over a cluster, all the submit logic has to be in rundist (or you can do it manually). I cannot generate these scripts and share them because each site is different.
The purpose of the scripts is to allow you to setup the configuration files once in the PAV install directory, then you symlink to the run directory (only rundist, runlocal, and config) and run it. Starting a new PAV run directory (i.e. another project) follows the same procedure. This is the way I run it for multiple projects I work on. You can just run Snakemake and not use these run scripts, they are meant to make it easier to scale (setup once, run many times with consistent parameters).
Are you distributing over a cluster or running on one machine? If it's a cluster, is it Slurm or SGE?
I cannot find config/runlocal.sh or config/rundist.sh, and cannot run this script. please help me! thanks.