/sra-tools

HowTo: Binary Installation

kwrodarmer edited this page Feb 19, 2015 · 4 revisions

The SRA Toolkit provides 64-bit binary installations for the Ubuntu and CentOS Linux distributions, for Mac OS X, and for Windows.

The current binaries for:

OS are available here
Windows [sratoolkit.current-win64.zip] (http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-win64.zip)
Ubuntu sratoolkit.current-ubuntu64.tar.gz
CentOS sratoolkit.current-centos_linux64.tar.gz
Mac OS X sratoolkit.current-mac64.tar.gz

For installing on Windows:

  1. Download the zip file from the link given above
  2. Extract it to your desktop, for example
  3. Open a command shell, for example Start/Run cmd.exe
  4. cd to the directory you extracted the zip file to, for example Desktop
  5. cd bin
  6. Test that the toolkit is functional:
fastq-dump --stdout -X 2 SRR390728

Within a few seconds, the command should produce this exact output (and nothing else):

Read 2 spots for SRR390728
Written 2 spots for SRR390728
@SRR390728.1 1 length=72
CATTCTTCACGTAGTTCTCGAGCCTTGGTTTTCAGCGATGGAGAATGACTTTGACAAGCTGAGAGAAGNTNC
+SRR390728.1 1 length=72
;;;;;;;;;;;;;;;;;;;;;;;;;;;9;;665142;;;;;;;;;;;;;;;;;;;;;;;;;;;;;96&&&&(
@SRR390728.2 2 length=72
AAGTAGGTCTCGTCTGTGTTTTCTACGAGCTTGTGTTCCAGCTGACCCACTCCCTGGGTGGGGGGACTGGGT
+SRR390728.2 2 length=72
;;;;;;;;;;;;;;;;;4;;;;3;393.1+4&&5&&;;;;;;;;;;;;;;;;;;;;;<9;<;;;;;464262

The installation processes for Mac OS X and the two Linux distributions are roughly identical.

1. Fetch the tar file from the canonical location at NCBI:
  • For Ubuntu,
wget --output-document sratoolkit.tar.gz http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
  • For CentOS,
wget --output-document sratoolkit.tar.gz http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-centos_linux64.tar.gz
  • For Mac OS X, (or use wget if you prefer)
curl --output sratoolkit.tar.gz http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-mac64.tar.gz
2. Extract the contents of the tar file:
tar -vxzf sratoolkit.tar.gz

Note the name of the directory that tar created. The name of this directory changes with each release and varies by platform, i.e. it follows the pattern sratoolkit.<release>-<platform> e.g. sratoolkit.2.4.0-1-mac64 for the 2.4.0-1 release for Mac OS X.

3. For convenience (and to show you where the binaries are) append the path to the binaries to your PATH environment variable:
export PATH=$PATH:$PWD/sratoolkit.2.4.0-1.mac64/bin
4. Verify that the binaries will be found by the shell:
which fastq-dump

This should produce output similar to:

/Users/JoeUser/sratoolkit.2.4.0-1.mac64/bin/fastq-dump
5. Test that the toolkit is functional:
fastq-dump --stdout SRR390728 | head -n 8

Within a few seconds, the command should produce this exact output (and nothing else):

@SRR390728.1 1 length=72
CATTCTTCACGTAGTTCTCGAGCCTTGGTTTTCAGCGATGGAGAATGACTTTGACAAGCTGAGAGAAGNTNC
+SRR390728.1 1 length=72
;;;;;;;;;;;;;;;;;;;;;;;;;;;9;;665142;;;;;;;;;;;;;;;;;;;;;;;;;;;;;96&&&&(
@SRR390728.2 2 length=72
AAGTAGGTCTCGTCTGTGTTTTCTACGAGCTTGTGTTCCAGCTGACCCACTCCCTGGGTGGGGGGACTGGGT
+SRR390728.2 2 length=72
;;;;;;;;;;;;;;;;;4;;;;3;393.1+4&&5&&;;;;;;;;;;;;;;;;;;;;;<9;<;;;;;464262