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README.md
README.md
 
 
compile_gpu.sh
compile_gpu.sh
 
 
init.sh
init.sh
 
 
patch_si_for_ks25_fork.diff
patch_si_for_ks25_fork.diff
 
 
setup_all.sh
setup_all.sh
 
 
setup_combinato.sh
setup_combinato.sh
 
 
setup_conda.sh
setup_conda.sh
 
 
setup_hdsort.sh
setup_hdsort.sh
 
 
setup_herdingspikes2.sh
setup_herdingspikes2.sh
 
 
setup_ironclust.sh
setup_ironclust.sh
 
 
setup_kilosort.sh
setup_kilosort.sh
 
 
setup_kilosort2.sh
setup_kilosort2.sh
 
 
setup_kilosort2_5.sh
setup_kilosort2_5.sh
 
 
setup_kilosort2_5_solve_zero_padding.sh
setup_kilosort2_5_solve_zero_padding.sh
 
 
setup_kilosort3.sh
setup_kilosort3.sh
 
 
setup_klusta.sh
setup_klusta.sh
 
 
setup_mease_elabftw.sh
setup_mease_elabftw.sh
 
 
setup_measelab.sh
setup_measelab.sh
 
 
setup_mountainsort4.sh
setup_mountainsort4.sh
 
 
setup_setup_jupyter.sh
setup_setup_jupyter.sh
 
 
setup_spyking_circus.sh
setup_spyking_circus.sh
 
 
setup_tridesclous.sh
setup_tridesclous.sh
 
 
setup_waveclus.sh
setup_waveclus.sh
 
 
setup_yass.sh
setup_yass.sh
 
 

README.md

Install Notes

Some notes on the installation on Helix, (hopefully) not relevant for the end user.

The initial idea is just to install everything in a folder, then share this location along with a script for the user to source, which puts everything in PATH, loads the relevant modules, and activates the conda env.

Location

All files are now installed on SDS:

  • /mnt/sds-hd/sd19b001/HPC_INSTALLATION_HELIX

Reproducibility

To recreate the HPC installation:

  • remove all files in /mnt/sds-hd/sd19b001/HPC_INSTALLATION_HELIX
  • run setup_all.sh which should reinstall everything from scratch
  • note: for ironclust gpu support, compile_gpu.sh also needs to run on a node with a GPU