PEP compatible

geofetch is a command-line tool that does two things when given one or more GEO/SRA accessions:

  • Downloads either raw or processed data from either GEO or SRA
  • Produces a standardized PEP sample annotation sheet of public metadata. This makes it really easy to run looper-compatible pipelines on public datasets by handling data acquisition and metadata formatting and standardization for you.

You can use it with the sra_convert pipeline, a pypiper pipeline that converts SRA files into BAM files.

Installing

pip install geofetch

Quick start

Now, run it on the command line:

geofetch --help

Next, check out the usage reference, or for a detailed walkthrough, head on over to the tutorial.