/Download_GSE_Files

automates process of downloading GSE files from public repository GEO

Primary LanguageJupyter Notebook

Download_GSE_Files

automates the process of downloading GSE files from public repository GEO

Setup

  1. cd <working directory>
  2. git clone https://github.com/laratse/Download_GSE_Files.git
  3. change permissions of downloadFiles and downloadGseFiles.sh
chmod +x downloadFiles Tools/downloadGseFiles.sh
  1. move Tools and downloadFiles to working directory

Usage

  1. Create your own directory to store the downloaded files. The directory name must be in the format of "xx..x_GSEnn..n" (no whitespace characters allowed, GSE id must be placed at the end of the string), eg. xyz_XYZ_GSE12345. When a corresponding directory is not provided, a default directory with the name DIR_GSEn...nn will be used instead
  2. create in.txt to enter the ID, one ID per line
  3. run the program by ./downloadFiles