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Al-Murphy / MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics
https://doi.org/doi:10.18129/B9.bioc.MungeSumstats
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Speed up VCF download #27

Closed bschilder closed 3 years ago

bschilder commented 3 years ago

Speed up VCF download from Open GWAS with axel at this step in import_sumstats:

if(vcf_download){
                    message("Downloading VCF ==> ",save_path) 
                    download.file(vcf_url, save_path)
                    # system(paste0("axel ",vcf_url," -o ",save_path))
                    # system(paste0("axel ",vcf_url,".tbi -o ",save_path,".tbi"))
                    vcf_url <- save_path 
                }
bschilder commented 3 years ago

Now implemented in import_sumstats via downloader and axel functions.

Automatically detects whether axel is installed, and if not, gives users instructions on how to install and then switches to using default download.file function.