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Repository sra_tools

Name: sra_tools

Owner: iuc

Synopsis: NCBI Sequence Read Archive toolkit utilities

Detailed description:

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.

Content homepage: https://github.com/ncbi/sra-tools

Development repository: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools

Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/iuc/sra_tools/7068f48d0ef9

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/sra_tools

Type: unrestricted

Revision: 18:7068f48d0ef9

This revision can be installed: True

Times cloned / installed: 7147

Repository README files - may contain important installation or license information

Readme files

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.