Mercurial > repos > jasmine_amir > sra_tools
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| author | jasmine_amir |
|---|---|
| date | Wed, 15 Feb 2023 16:33:01 -0500 |
| parents | 878e5d4becef |
| children |
| rev | line source |
|---|---|
| jasmine_amir@0 | 1 The Galaxy tool wrappers contained in this tool shed repository rely on software developed by |
| jasmine_amir@0 | 2 the NCBI: https://github.com/ncbi/sra-tools. |
| jasmine_amir@0 | 3 |
| jasmine_amir@0 | 4 NCBI Sequence Read Archive Toolkit: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software |
| jasmine_amir@0 | 5 |
| jasmine_amir@0 | 6 # Installation of Aspera connect ascp binary |
| jasmine_amir@0 | 7 |
| jasmine_amir@0 | 8 The sra-tools suite is ready to benefit from increased transfer speed and reliability by using Aspera Connect ascp. |
| jasmine_amir@0 | 9 To benefit, download the ascp commandline client, and place ascp and the required ssh keys into a PATH accessible to galaxys job handler. |
| jasmine_amir@0 | 10 |
| jasmine_amir@0 | 11 A convenience package for linux and OS X is available at https://toolshed.g2.bx.psu.edu/view/mvdbeek/package_ascp_3/e109f0ec22c3 . |
| jasmine_amir@0 | 12 It suffices to copy the contents of the $INSTALL_DIR/bin into PATH. |
| jasmine_amir@0 | 13 |
| jasmine_amir@0 | 14 Alternatively go to http://downloads.asperasoft.com/connect2/ . |
| jasmine_amir@0 | 15 |
| jasmine_amir@0 | 16 Aspera connect is not provided by the IUC due to its closed-source nature. |
| jasmine_amir@0 | 17 |
| jasmine_amir@0 | 18 # Firewall settings for highspeed transfer |
| jasmine_amir@0 | 19 |
| jasmine_amir@0 | 20 To benefit from increased transfer speeds using ascp3 your local firewall must permit UDP data transfer in both |
| jasmine_amir@0 | 21 directions on ports 33001-33009 for the following IP ranges: |
| jasmine_amir@0 | 22 |
| jasmine_amir@0 | 23 130.14.*.* |
| jasmine_amir@0 | 24 |
| jasmine_amir@0 | 25 165.112.*.* |
| jasmine_amir@0 | 26 |
| jasmine_amir@0 | 27 The firewall must also allow ssh traffic outbound to NCBI. |
| jasmine_amir@0 | 28 The wrapper will fall back to http download if these requirements are not met. |
| jasmine_amir@0 | 29 |
| jasmine_amir@0 | 30 CONTROLLED-ACCESS DATA |
| jasmine_amir@0 | 31 |
| jasmine_amir@0 | 32 Encrypted, controlled-access data is not supported. |