Can't find the `runlocal` script

[panosioannidis]

I'm trying to run the PAV example, but cannot find the runlocal script which should be at the root of the PAV repository that I cloned. The only file I find is runlocal.sh which, however, is not located at the PAV root; it's in files/run_scripts/.

Am I missing something?

[paudano]

Look at README.md for instructions on running PAV. The easiest way to run PAV is through the Docker or Singularity/Apptainer images.

I realize now that I did not update NATIVE_INSTALL.md, and it still references the runlocal scripts. You can symlink Snakefile (and optionally profiles if you are using it), then run Snakemake directly. The Snakefile was updated to find all the PAV files through a symbolic link. runlocal and rundist was a convoluted way to run PAV, so it was removed some time ago.