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author bgruening
date Thu, 05 Sep 2013 04:58:21 -0400
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1 These are Galaxy wrappers for common unix text-processing tools
2 ===============================================================
3
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 ).
6
7
8 The tools are:
9
10 * awk - The AWK programmning language ( http://www.gnu.org/software/gawk/ )
11 * sed - Stream Editor ( http://sed.sf.net )
12 * grep - Search files ( http://www.gnu.org/software/grep/ )
13 * sort_columns - Sorting every line according to there columns
14 * GNU Coreutils programs ( http://www.gnu.org/software/coreutils/ ):
15 * sort - sort files
16 * join - join two files, based on common key field.
17 * cut - keep/discard fields from a file
18 * unsorted_uniq - keep unique/duplicated lines in a file
19 * sorted_uniq - keep unique/duplicated lines in a file
20 * head - keep the first X lines in a file.
21 * tail - keep the last X lines in a file.
22
23 Few improvements over the standard tools:
24
25 * EasyJoin - A Join tool that does not require pre-sorted the files ( https://github.com/agordon/filo/blob/scripts/src/scripts/easyjoin )
26 * Multi-Join - Join multiple (>2) files ( https://github.com/agordon/filo/blob/scripts/src/scripts/multijoin )
27 * Find_and_Replace - Find/Replace text in a line or specific column.
28 * Grep with Perl syntax - uses grep with Perl-Compatible regular expressions.
29 * HTML'd Grep - grep text in a file, and produced high-lighted HTML output, for easier viewing ( uses https://github.com/agordon/filo/blob/scripts/src/scripts/sort-header )
30
31
32 Requirements
33 ------------
34
35 1. Coreutils vesion 8.19 or later.
36 2. AWK version 4.0.1 or later.
37 3. SED version 4.2 *with* a special patch
38 4. Grep with PCRE support
39
40 These will be installed automatically with the Galaxy Tool Shed.
41
42
43 -------------------
44 NOTE About Security
45 -------------------
46
47 The included tools are secure (barring unintentional bugs):
48 The main concern might be executing system commands with awk's "system" and sed's "e" commands,
49 or reading/writing arbitrary files with awk's redirection and sed's "r/w" commands.
50 These commands are DISABLED using the "--sandbox" parameter to awk and sed.
51
52 User trying to run an awk program similar to:
53 BEGIN { system("ls") }
54 Will get an error (in Galaxy) saying:
55 fatal: 'system' function not allowed in sandbox mode.
56
57 User trying to run a SED program similar to:
58 1els
59 will get an error (in Galaxy) saying:
60 sed: -e expression #1, char 2: e/r/w commands disabled in sandbox mode
61
62 That being said, if you do find some vulnerability in these tools, please let me know and I'll try fix them.
63
64 ------------
65 Installation
66 ------------
67
68 Should be done with the Galaxy `Tool Shed`_.
69
70 .. _`Tool Shed`: http://wiki.galaxyproject.org/Tool%20Shed
71
72
73 ----
74 TODO
75 ----
76
77 - unit-tests
78 - uniqu will get a new --group funciton with the 8.22 release, its currently commended out
79 - also shuf will get a major improved performance with large files http://git.savannah.gnu.org/gitweb/?p=coreutils.git;a=commit;h=20d7bce0f7e57d9a98f0ee811e31c757e9fedfff
80 we can remove the random feature from sort and use shuf instead
81 - move some advanced settings under a conditional, for example the cut tools offers to cut bytes
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