2 Installing SRA Toolkit

2.1 Navigate to Installation Directory

Navigate to the directory where you want to install the tools, preferably the home directory. To install the SRA Toolkit, follow these steps:

curl -LO https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.0/sratoolkit.3.0.0-mac64.tar.gz
tar -xf sratoolkit.3.0.0-mac64.tar.gz
export PATH=$HOME/sratoolkit.3.0.0-mac64/bin/:$PATH

2.2 Create a cache root directory

mkdir -p ~/ncbi
echo '/repository/user/main/public/root = "cache_directory"' > ~/ncbi/user-settings.mkfg

2.3 Confirm sra toolkit configuration

• The vdb-config -i command below will display a blue colored dialog.
• Use tab or click c to navigate to cache tab.
• Review the configuration then save s and exit x.

vdb-config -i

A screenshot of the SRA configuration.

For more information click here.

2.4 Alternative Method

You can create an environment and install essential tools in it. For example, you can create an environment named sradb using an environment.yml file:

name: sradb
channels:
  - conda-forge
  - bioconda
dependencies:
  - sra-tools
  - entrez-direct
  - pysradb

mamba create -c bioconda -c conda-forge sradb -file environment.yml