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stephenslab / susie-paper

Experiments on SuSiE ("sum of single effects") regression.
https://stephenslab.github.io/susie-paper
MIT License
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Meta-database replacement for compatibility with newer DSC versions (0.3.10+) #2

Closed gaow closed 4 years ago

gaow commented 4 years ago

See https://github.com/stephenslab/dsc/issues/211 for the error report. The solution is to run the benchmark with -s all option to skip all runs just updating the meta-data, but using the gene list gtex-manifest.txt that I actually used for the paper, not the toy list I provide in this repo. For this reason I generated these replacements db files and upload it here.

Here are step-by-step instruction to upgrade and run this repo using latest DSC version (currently 0.4.0):

  1. Download these meta databases and replace the original susie_comparison.db and hard_case.db with them;
  2. git pull this repository to make sure all files are up-to-date;
  3. pip install dsc -U to update to latest DSC release;
  4. In R, run devtools::install_github("stephenslab/dsc",subdir = "dscrutils", force = TRUE) to update to latest dscrutils;
  5. Optionally, you can build again the docker image and run from docker, see details under "Build the docker image" section on this page.

You should then be able to follow instructions on this website without errors due to DSC version updates.