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02. Installing SRA Toolkit

skripche edited this page Aug 29, 2019 · 5 revisions

Installing in the CLOUD

The cloud providers allow you to create an instance with many different operating systems. In order to successfully install the toolkit you need to choose the correct installation script and the following steps will help you do so.

Please run the following command in your terminal window:

which apt-get

If your linux terminal displays something like the following:

/usr/bin/apt-get

Please download this install script to your cloud machine by using the command :

wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.10.0/setup-apt.sh

Otherwise, please run this command:

wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.10.0/setup-yum.sh

Once you have downloaded the script to your cloud instance, please run either:

sudo sh setup-apt.sh

or

sudo sh setup-yum.sh

If the above commands do not work due to an error requiring sudo permissions, please login into your cloud instance using an account with sudo permissions.

The installation of all required dependencies can take several minutes.

Once the script is done running, please run:

source /etc/profile.d/sra-tools.sh

Your installation is now done and you can go on to the next step of quick configuring your toolkit.

Installing Locally

Installation for Linux systems has not changed, please visit Download section and download the appropriate version of the tarball for your operating system.

You will need to extract the tools from the tarball like so:

tar xzf sratoolkit.2.10.0-ubuntu64.tar.gz

If you downloaded the CentOS tarball please change the name appropriately.

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