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author iuc
date Sun, 06 Dec 2015 09:04:37 -0500
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1 The Galaxy tool wrappers contained in this tool shed repository rely on software developed by
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2 the NCBI: http://github.com/ncbi/sra-tools.
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4 NCBI Sequence Read Archive: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
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5 Use of SRA Toolkit software herein should comply with the GPL v2 or greater.
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7 Copyright (C) 2013 Matthew Shirley
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9 This program is free software: you can redistribute it and/or modify
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10 it under the terms of the GNU General Public License as published by
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11 the Free Software Foundation, either version 2 of the License, or
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12 (at your option) any later version.
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14 This program is distributed in the hope that it will be useful,
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15 but WITHOUT ANY WARRANTY; without even the implied warranty of
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16 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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17 GNU General Public License for more details.
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19 You should have received a copy of the GNU General Public License
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20 along with this program. If not, see <http://www.gnu.org/licenses/>.
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22 # INSTALLATION
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24 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.
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26 *Build Requirements*
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28 - bash
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29 - make
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30 - gcc
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31 - g++
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32 - libxml2
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34 On a Debian OS use:
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36 apt-get install build-essential libxml2-dev
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38 On a Mac with [command line tools](https://developer.apple.com/downloads/index.action) installed:
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40 brew install libxml2
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42 # Installation of Aspera connect ascp binary
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44 The sra-tools suite is ready to benefit from increased transfer speed and reliability by using Aspera Connect ascp.
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45 To benefit, download the ascp commandline client, and place ascp and the required ssh keys into a PATH accessible to galaxys job handler.
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47 A convenience package for linux and OS X is available at https://toolshed.g2.bx.psu.edu/view/mvdbeek/package_ascp_3/e109f0ec22c3 .
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48 It suffices to copy the contents of the $INSTALL_DIR/bin into PATH.
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50 Alternatively go to http://downloads.asperasoft.com/connect2/ .
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52 Aspera connect is not provided by the IUC due to its closed-source nature.
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54 # Firewall settings for highspeed transfer
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56 To benefit from increased transfer speeds using ascp3 your local firewall must permit UDP data transfer in both
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57 directions on ports 33001-33009 for the following IP ranges:
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59 130.14.*.*
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61 165.112.*.*
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63 The firewall must also allow ssh traffic outbound to NCBI.
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64 The wrapper will fall back to http download if these requirements are not met.
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66 CONTROLLED-ACCESS DATA
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68 Encrypted, controlled-access data is not supported.