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author bgruening
date Wed, 07 Jan 2015 11:10:52 -0500
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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 ). 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
7 text manipulation tool to this repository.
6 8
7 9
8 Tools: 10 Tools:
9 11
10 * awk - The AWK programmning language ( http://www.gnu.org/software/gawk/ ) 12 * awk - The AWK programmning language ( http://www.gnu.org/software/gawk/ )
31 33
32 34
33 Requirements 35 Requirements
34 ------------ 36 ------------
35 37
36 1. Coreutils vesion 8.19 or later. 38 1. Coreutils vesion 8.22 or later.
37 2. AWK version 4.0.1 or later. 39 2. AWK version 4.0.1 or later.
38 3. SED version 4.2 *with* a special patch 40 3. SED version 4.2 *with* a special patch
39 4. Grep with PCRE support 41 4. Grep with PCRE support
40 42
41 These will be installed automatically with the Galaxy `Tool Shed`_. 43 These will be installed automatically with the Galaxy `Tool Shed`_.
80 82
81 ---- 83 ----
82 TODO 84 TODO
83 ---- 85 ----
84 86
85 - unit-tests 87 - add shuf
86 - uniqu will get a new --group funciton with the 8.22 release, its currently commended out
87 - also shuf will get a major improved performance with large files http://git.savannah.gnu.org/gitweb/?p=coreutils.git;a=commit;h=20d7bce0f7e57d9a98f0ee811e31c757e9fedfff
88 we can remove the random feature from sort and use shuf instead 88 we can remove the random feature from sort and use shuf instead
89 - move some advanced settings under a conditional, for example the cut tools offers to cut bytes 89 - move some advanced settings under a conditional, for example the cut tools offers to cut bytes
90 - cut wrapper has some output conditional magic for interval files, that needs to be checked 90 - cut wrapper has some output conditional magic for interval files, that needs to be checked
91 - comm wrapper, see the Galaxy default one 91 - comm wrapper, see the Galaxy default one
92 - evaluate the join wrappers against the Galaxy ones, maybe we should drop them 92 - evaluate the join wrappers against the Galaxy ones, maybe we should drop them
95 ------- 95 -------
96 License 96 License
97 ------- 97 -------
98 98
99 * Copyright (c) 2009-2013 A. Gordon (gordon <at> cshl dot edu) 99 * Copyright (c) 2009-2013 A. Gordon (gordon <at> cshl dot edu)
100 * Copyright (c) 2013 B. Gruening (bjoern dot gruening <at> gmail dot com) 100 * Copyright (c) 2013-2015 B. Gruening (bjoern dot gruening <at> gmail dot com)
101 101
102 102
103 Permission is hereby granted, free of charge, to any person obtaining 103 Permission is hereby granted, free of charge, to any person obtaining
104 a copy of this software and associated documentation files (the 104 a copy of this software and associated documentation files (the
105 "Software"), to deal in the Software without restriction, including 105 "Software"), to deal in the Software without restriction, including