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comparison readme.rst @ 9:d9819ccb9ca7 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
author bgruening
date Tue, 30 Jun 2015 17:47:36 -0400
parents 8928e6d1e7ba
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8:fa7f88da29d7 9:d9819ccb9ca7
1 Galaxy wrappers for common unix text-processing tools 1 Galaxy wrappers for common unix text-processing tools
2 ===================================================== 2 =====================================================
3 3
4 The initial work was done by Assaf Gordon and Greg Hannon's lab ( http://hannonlab.cshl.edu ) 4 The initial work was done by Assaf Gordon and Greg Hannon's lab ( http://hannonlab.cshl.edu )
5 in Cold Spring Harbor Laboratory ( http://www.cshl.edu ). In late 2013 maintainence and 5 in Cold Spring Harbor Laboratory ( http://www.cshl.edu ). In late 2013 maintainence and
6 further development was taken over by Bjoern Gruening. Feel free to contribute any general purpose 6 further development was taken over by Bjoern Gruening. Feel free to contribute any general purpose
7 text manipulation tool to this repository. 7 text manipulation tool to this repository.
8 8
9 9
10 Tools: 10 Tools:
56 or reading/writing arbitrary files with awk's redirection and sed's "r/w" commands. 56 or reading/writing arbitrary files with awk's redirection and sed's "r/w" commands.
57 These commands are DISABLED using the "--sandbox" parameter to awk and sed. 57 These commands are DISABLED using the "--sandbox" parameter to awk and sed.
58 58
59 User trying to run an awk program similar to:: 59 User trying to run an awk program similar to::
60 60
61 BEGIN { system("ls") } 61 BEGIN { system("ls") }
62 62
63 Will get an error (in Galaxy) saying:: 63 Will get an error (in Galaxy) saying::
64 64
65 fatal: 'system' function not allowed in sandbox mode. 65 fatal: 'system' function not allowed in sandbox mode.
66 66
67 User trying to run a SED program similar to:: 67 User trying to run a SED program similar to::
68 68
69 1els 69 1els
70 70
71 will get an error (in Galaxy) saying:: 71 will get an error (in Galaxy) saying::
72 72
73 sed: -e expression #1, char 2: e/r/w commands disabled in sandbox mode 73 sed: -e expression #1, char 2: e/r/w commands disabled in sandbox mode
74 74
75 That being said, if you do find some vulnerability in these tools, please let me know and I'll try fix them. 75 That being said, if you do find some vulnerability in these tools, please let me know and I'll try fix them.
76 76
77 ------------ 77 ------------
78 Installation 78 Installation
101 101
102 * Copyright (c) 2009-2013 A. Gordon (gordon <at> cshl dot edu) 102 * Copyright (c) 2009-2013 A. Gordon (gordon <at> cshl dot edu)
103 * Copyright (c) 2013-2015 B. Gruening (bjoern dot gruening <at> gmail dot com) 103 * Copyright (c) 2013-2015 B. Gruening (bjoern dot gruening <at> gmail dot com)
104 104
105 105
106 Permission is hereby granted, free of charge, to any person obtaining 106 Permission is hereby granted, free of charge, to any person obtaining
107 a copy of this software and associated documentation files (the 107 a copy of this software and associated documentation files (the
108 "Software"), to deal in the Software without restriction, including 108 "Software"), to deal in the Software without restriction, including
109 without limitation the rights to use, copy, modify, merge, publish, 109 without limitation the rights to use, copy, modify, merge, publish,
110 distribute, sublicense, and/or sell copies of the Software, and to 110 distribute, sublicense, and/or sell copies of the Software, and to
111 permit persons to whom the Software is furnished to do so, subject to 111 permit persons to whom the Software is furnished to do so, subject to
112 the following conditions: 112 the following conditions:
113 113
114 The above copyright notice and this permission notice shall be 114 The above copyright notice and this permission notice shall be
115 included in all copies or substantial portions of the Software. 115 included in all copies or substantial portions of the Software.
116 116
117 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 117 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
118 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 118 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
119 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 119 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
120 IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY 120 IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
121 CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 121 CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
122 TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 122 TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
123 SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 123 SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
124