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02. Installing SRA Toolkit

skripche edited this page Feb 23, 2020 · 9 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. Proceed to the Quick Configuration Guide
  7. 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. Proceed to the Quick Configuration Guide
6. 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