Mercurial > repos > jasmine_amir > sra_tools
comparison README.rst @ 0:878e5d4becef
planemo upload
| author | jasmine_amir |
|---|---|
| date | Thu, 02 Feb 2023 18:11:05 -0500 |
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| -1:000000000000 | 0:878e5d4becef |
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| 1 The Galaxy tool wrappers contained in this tool shed repository rely on software developed by | |
| 2 the NCBI: https://github.com/ncbi/sra-tools. | |
| 3 | |
| 4 NCBI Sequence Read Archive Toolkit: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software | |
| 5 | |
| 6 # Installation of Aspera connect ascp binary | |
| 7 | |
| 8 The sra-tools suite is ready to benefit from increased transfer speed and reliability by using Aspera Connect ascp. | |
| 9 To benefit, download the ascp commandline client, and place ascp and the required ssh keys into a PATH accessible to galaxys job handler. | |
| 10 | |
| 11 A convenience package for linux and OS X is available at https://toolshed.g2.bx.psu.edu/view/mvdbeek/package_ascp_3/e109f0ec22c3 . | |
| 12 It suffices to copy the contents of the $INSTALL_DIR/bin into PATH. | |
| 13 | |
| 14 Alternatively go to http://downloads.asperasoft.com/connect2/ . | |
| 15 | |
| 16 Aspera connect is not provided by the IUC due to its closed-source nature. | |
| 17 | |
| 18 # Firewall settings for highspeed transfer | |
| 19 | |
| 20 To benefit from increased transfer speeds using ascp3 your local firewall must permit UDP data transfer in both | |
| 21 directions on ports 33001-33009 for the following IP ranges: | |
| 22 | |
| 23 130.14.*.* | |
| 24 | |
| 25 165.112.*.* | |
| 26 | |
| 27 The firewall must also allow ssh traffic outbound to NCBI. | |
| 28 The wrapper will fall back to http download if these requirements are not met. | |
| 29 | |
| 30 CONTROLLED-ACCESS DATA | |
| 31 | |
| 32 Encrypted, controlled-access data is not supported. |