get_ebi_fastqs: Download fastqs from EBI

In alexvpickering/GEOfastq: Downloads ENA Fastqs With GEO Accessions

Description

Much faster to use aspera than ftp

Usage

get_ebi_fastqs(
  srp_meta,
  srr_name,
  data_dir,
  method = c("ftp", "aspera"),
  max_rate = "300m"
)

Arguments

srp_meta	data.frame with SRP meta info. Returned from crawl_gsms.
srr_name	Run accession as string.
data_dir	Path to folder that fastq files will be downloaded to. Will be created if doesn't exist.
method	One of 'aspera' or 'ftp'. 'aspera' is generally faster but requires the ascp command line utility to be on your path and in the authors experience frequently stalls.
max_rate	Used when method = 'aspera' only. Sets the target transfer rate. The default is '300m'.

Value

Integer return code from ascp or download.file.

alexvpickering/GEOfastq documentation built on Oct. 11, 2021, 6:44 p.m.