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This repository was archived by the owner on Jan 29, 2026. It is now read-only.
This repository was archived by the owner on Jan 29, 2026. It is now read-only.

GRCh38 not installing #19

@gevro

Description

@gevro

Hi,
I'm getting this error:

> install("GRCh38", rsync=FALSE, bash=TRUE)
Tool       | Installed 
-----------------------
curl       | True      
wget       | True      
rsync      | True      
INFO - Downloading GRCh38...
INFO - Attempt to download from alexandrovlab failed: [Errno 104] Connection reset by peer
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
curl: (56) Recv failure: Connection reset by peer
ERROR - Curl download failed with error: Command '['curl', '-o', '/gpfs/data/elab/bin/Rconda/lib/python3.13/site-packages/SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh38.tar.gz', 'ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator//GRCh38.tar.gz']' returned non-zero exit status 56..
ERROR - Curl download failed with error: Command '['curl', '-o', '/gpfs/data/elab/bin/Rconda/lib/python3.13/site-packages/SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh38.tar.gz', 'ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator//GRCh38.tar.gz']' returned non-zero exit status 56.
INFO - Attempt to download from sanger failed: [Errno 104] Connection reset by peer
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:--  0:00:10 --:--:--     0
curl: (56) Recv failure: Connection reset by peer
ERROR - Curl download failed with error: Command '['curl', '-o', '/gpfs/data/elab/bin/Rconda/lib/python3.13/site-packages/SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh38.tar.gz', 'ftp://ngs.sanger.ac.uk/scratch/project/mutographs/SigProf//GRCh38.tar.gz']' returned non-zero exit status 56..
ERROR - Curl download failed with error: Command '['curl', '-o', '/gpfs/data/elab/bin/Rconda/lib/python3.13/site-packages/SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh38.tar.gz', 'ftp://ngs.sanger.ac.uk/scratch/project/mutographs/SigProf//GRCh38.tar.gz']' returned non-zero exit status 56.
Error in py_call_impl(callable, call_args$unnamed, call_args$named) : 
  FileNotFoundError: [Errno 2] No such file or directory: '/gpfs/data/elab/bin/Rconda/lib/python3.13/site-packages/SigProfilerMatrixGenerator/references/chromosomes/tsb/GRCh38.tar.gz'
Run `reticulate::py_last_error()` for details.

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