Mercurial > repos > iuc > sra_tools
diff README.rst @ 0:b723c120161a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
author | iuc |
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date | Sun, 06 Dec 2015 09:04:37 -0500 |
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children | 7068f48d0ef9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Sun Dec 06 09:04:37 2015 -0500 @@ -0,0 +1,68 @@ +The Galaxy tool wrappers contained in this tool shed repository rely on software developed by +the NCBI: http://github.com/ncbi/sra-tools. + +NCBI Sequence Read Archive: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. +Use of SRA Toolkit software herein should comply with the GPL v2 or greater. + +Copyright (C) 2013 Matthew Shirley + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + +# INSTALLATION + +This software release was designed to install using the Galaxy toolshed under Linux and MacOS operating systems on Intel x86-compatible 32/64 bit architectures. + +*Build Requirements* + +- bash +- make +- gcc +- g++ +- libxml2 + +On a Debian OS use: + + apt-get install build-essential libxml2-dev + +On a Mac with [command line tools](https://developer.apple.com/downloads/index.action) installed: + + brew install libxml2 + +# 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.