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Repository sra_tools
Name: sra_tools
Owner: iuc
Synopsis: NCBI Sequence Read Archive toolkit utilities
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for
using data in the INSDC Sequence Read Archives.
CONTROLLED-ACCESS DATA Encrypted, controlled-access data is not supported in
this version of the SRA Toolkit Galaxy tools.
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/sra_tools
Type: unrestricted
Revision: 34:e407b9da183a
This revision can be installed: True
Times cloned / installed: 6322

Repository README files - may contain important installation or license information

The Galaxy tool wrappers contained in this tool shed repository rely on software developed by the NCBI: https://github.com/ncbi/sra-tools.

NCBI Sequence Read Archive Toolkit: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

# Installation of Aspera connect ascp binary

The sra-tools suite is ready to benefit from increased transfer speed and reliability by using Aspera Connect ascp. To benefit, download the ascp commandline client, and place ascp and the required ssh keys into a PATH accessible to galaxys job handler.

A convenience package for linux and OS X is available at https://toolshed.g2.bx.psu.edu/view/mvdbeek/package_ascp_3/e109f0ec22c3 . It suffices to copy the contents of the $INSTALL_DIR/bin into PATH.

Alternatively go to http://downloads.asperasoft.com/connect2/ .

Aspera connect is not provided by the IUC due to its closed-source nature.

# Firewall settings for highspeed transfer

To benefit from increased transfer speeds using ascp3 your local firewall must permit UDP data transfer in both directions on ports 33001-33009 for the following IP ranges:

130.14.*.*

165.112.*.*

The firewall must also allow ssh traffic outbound to NCBI. The wrapper will fall back to http download if these requirements are not met.

CONTROLLED-ACCESS DATA

Encrypted, controlled-access data is not supported.

Contents of this repository

Name Description Version Minimum Galaxy Version
format from NCBI SRA 3.0.8+galaxy1 22.01
format from NCBI SRA 3.0.8+galaxy1 22.01
format from NCBI SRA 3.0.8+galaxy1 22.01

Categories
Data Source - Tools for retrieving data from external data sources
Fastq Manipulation - Tools for manipulating fastq data