Mercurial > repos > yhoogstrate > package_unafold_3_8

annotate tool_dependencies.xml @ 0:1934c4216597 draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 9ac0b453ceb7370d9ae50bc2c26ae06c905c736b
author yhoogstrate
date Tue, 16 Jun 2015 09:14:24 -0400
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1934c4216597 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 9ac0b453ceb7370d9ae50bc2c26ae06c905c736b
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1 <?xml version="1.0"?>
1934c4216597 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 9ac0b453ceb7370d9ae50bc2c26ae06c905c736b
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2 <tool_dependency>
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3 <package name="unafold" version="3.8">
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4 <install version="1.0">
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5 <actions>
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6 <action type="shell_command">
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7 wget http://homepages.rpi.edu/~zukerm/download/unafold-3.8.tar.gz &amp;&amp;
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8 tar -zxvf unafold-3.8.tar.gz &amp;&amp;
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9 cd unafold-3.8 &amp;&amp;
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10 ./configure --prefix=$INSTALL_DIR &amp;&amp;
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11 make &amp;&amp;
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12 make install
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13 </action>
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14 <action type="set_environment">
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15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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16 <!--<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>-->
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17 </action>
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18 </actions>
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19 </install>
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20 <readme>
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21 Downloads and installs UNAFold.
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22
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23 Prerequisites:
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24 - perl
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25 - wget
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26 - tar
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27 - gnu-autotools (make)
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28
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29
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30 License
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31 -------
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32
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33 UNAFold 3.x ACADEMIC NON-COMMERCIAL USE LICENSE AGREEMENT
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34
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35 1. UNAFold 3.x is the work of Drs. Nicholas R. Markham and Michael Zuker. The
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36 copyright in UNAFold 3.x is owned by RENSSELAER POLYTECHNIC INSTITUTE.
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37
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38 2. This is a legal agreement between you, RECIPIENT, and RENSSELAER POLYTECHNIC
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39 INSTITUTE. By accepting, receiving, and using UNAFold 3.x, you agree to be
1934c4216597 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 9ac0b453ceb7370d9ae50bc2c26ae06c905c736b
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40 bound by all of its terms. If you do not agree to all of the terms of this
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41 Agreement, please DO NOT download the software; or, if you have already done
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42 so, please delete all of the source code, documentation and compiled programs
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43 associated with UNAFold 3.x.
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44
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45 3. UNAFold 3.x is provided to RECIPIENT as source code. RENSSELAER POLYTECHNIC
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46 INSTITUTE grants to RECIPIENT a royalty free, non-exclusive, and non-
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47 transferable license to compile, install, use UNAFold for internal research
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48 only. RECIPIENT acknowledges that UNAFold 3.x is a research tool that is
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49 provided free of charge and only provided "as is." RENSSELAER POLYTECHNIC
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50 INSTITUTE, its faculty, employees, or students, or former employees who have
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51 developed UNAFold 3.x, have no obligation to assist RECIPIENT in its use,
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52 correction, modification, or enhancement and are without any obligation to
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53 provide any updates. RECIPIENT may also offer UNAFold 3.x to the public over
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54 a web server provided the program resides on a server at RECIPIENT's
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55 institution and users are not able to download or modify the program.
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56
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57 4. The title and copyright to UNAFold 3.x and any associated programs and
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58 documentation shall remain with RENSSELAER POLYTECHNIC INSTITUTE. RECIPIENT
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59 agrees to preserve same. RECIPIENT agrees not to make any copies of UNAFold
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60 except for use in RECIPIENT's laboratory without RENSSELAER POLYTECHNIC
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61 INSTITUTE's prior written permission. Written permission can be obtained by
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62 contacting Rensselaer Polytechnic Institute's Office of Technology
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63 Commercialization by e-mail at burtok2@rpi.edu, or by telephone at 518-276-
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64 3675. RECIPIENT agrees to place the appropriate copyright notice on any such
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65 copies.
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66
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67 5. RECIPIENT may not modify UNAFold 3.x, except to fix minor errors, or create
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68 derivative works without RENSSELAER POLYTECHNIC INSTITUTE's permission.
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69 Please send all requests for modification to markhn@rpi.edu and
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70 zukerm@rpi.edu. Errors and bugs that are found should be reported to Nick
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71 Markham and Michael Zuker, whether or not they are corrected.
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72
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73 6. RECIPIENT shall not distribute UNAFold 3.x to other laboratories within
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74 RECIPIENT's institution. RECIPIENT shall not transfer UNAFold 3.x to another
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75 location or person outside of RECIPIENT's institution without RENSSELAER
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76 POLYTECHNIC INSTITUTE's prior written permission. Please send all requests
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77 for distribution to markhn@rpi.edu and zukerm@rpi.edu.
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78
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79 7. If RENSSELAER POLYTECHNIC INSTITUTE grants RECIPIENT permission to distribute
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80 UNAFold 3.x, under Paragraph 6, RECIPIENT shall only export UNAFold 3.x or
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81 any part thereof, directly or indirectly, to any country where such export or
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82 reexport is authorized in full compliance with the laws of the United States
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83 of America.
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84
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85 8. RECIPENT shall cite the following publications in any abstract, paper, or
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86 presentation referencing UNAFold:
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87
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88 a. N. Markham &amp; M. Zuker. (2003) DINAMelt web server for nucleic acid melting
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89 prediction. Nucleic Acids Res. 33:W577-W581.
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90
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91 9. RECIPIENT acknowledges that as UNAFold 3.x is a research tool and provided
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92 free of charge, it is only provided "as is." RENSSELAER POLYTECHNIC
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93 INSTITUTE, its faculty, employees, or students, have no obligation to assist
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94 RECIPIENT in its use, correction, modification, or enhancement and are
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95 without any obligation to provide any updates.
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96
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97 10. RENSSELAER POLYTECHNIC INSTITUTE MAKES NO REPRESENTATIONS AND EXTENDS NO
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98 WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED. THERE ARE NO EXPRESS OR
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99 IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS OF UNAFold 3.x FOR A
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100 PARTICULAR PURPOSE, OR THAT THE USE OF UNAFold 3.x WILL NOT INFRINGE ANY
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101 PATENT, COPYRIGHT, TRADEMARK, TRADE SECRET, OR OTHER INTELLECTUAL PROPERTY
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102 RIGHTS OF ANOTHER PARTY, OR ANY OTHER EXPRESS OR IMPLIED WARRANTIES.
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103 RENSSELAER POLYTECHNIC INSTITUTE WILL NOT BE LIABLE TO RECIPIENT FOR ANY
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104 CLAIMS OR DAMAGES ARISING FROM YOUR RECIPIENT'S OF UNAFold 3.x, ANY CLAIM
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105 FOR ANY LOSS OR INTERRUPTION OF BUSINESS, OR FOR ANY INDIRECT, SPECIAL, OR
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106 CONSEQUENTIAL DAMAGES OF ANY KIND.
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107 </readme>
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108 </package>
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109 </tool_dependency>