diff README @ 0:631dfde45073 draft default tip

First tool-shed public version

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+These are Galaxy wrappers for common unix text-processing tools.
+
+Source:
+http://hannonlab.cshl.edu/galaxy_unix_tools/index.html
+
+Contact: gordon at cshl dot edu
+
+NOTE: You must install some programs manually. See below for details.
+
+The tools are:
+
+* awk - The AWK programmning language ( http://www.gnu.org/software/gawk/ )
+* sed - Stream Editor ( http://sed.sf.net )
+* grep - Search files ( http://www.gnu.org/software/grep/ )
+* GNU Coreutils programs ( http://www.gnu.org/software/coreutils/ ):
+  * sort - sort files
+  * join - join two files, based on common key field.
+  * cut  - keep/discard fields from a file
+  * uniq - keep unique/duplicated lines in a file
+  * head - keep the first X lines in a file.
+  * tail - keep the last X lines in a file.
+
+Few improvements over the standard tools:
+
+  * EasyJoin - A Join tool that does not require pre-sorted the files ( https://github.com/agordon/filo/blob/scripts/src/scripts/easyjoin )
+  * Multi-Join - Join multiple (>2) files ( https://github.com/agordon/filo/blob/scripts/src/scripts/multijoin )
+  * Sort-Header - Sort a file, while maintaining the first line as header line ( https://github.com/agordon/filo/blob/scripts/src/scripts/sort-header )
+  * Find_and_Replace - Find/Replace text in a line or specific column.
+  * Grep with Perl syntax - uses grep with Perl-Compatible regular expressions.
+  * 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 )
+
+
+Requirements
+============
+1. Coreutils vesion 8.19 or later.
+2. AWK version 4.0.1 or later.
+3. SED version 4.2 *with* a special patch
+4. Grep with PCRE support
+
+
+NOTE About Security
+===================
+The included tools are secure (barring unintentional bugs):
+The main concern might be executing system commands with awk's "system" and sed's "e" commands,
+or reading/writing arbitrary files with awk's redirection and sed's "r/w" commands.
+These commands are DISABLED using the "--sandbox" parameter to awk and sed.
+
+User trying to run an awk program similar to:
+ BEGIN { system("ls") }
+Will get an error (in Galaxy) saying:
+ fatal: 'system' function not allowed in sandbox mode.
+
+User trying to run a SED program similar to:
+ 1els
+will get an error (in Galaxy) saying:
+ sed: -e expression #1, char 2: e/r/w commands disabled in sandbox mode
+
+That being said, if you do find some vulnerability in these tools, please let me know and I'll fix them.
+
+
+Installation
+============
+
+## GNU coreutils
+ wget http://ftp.gnu.org/gnu/coreutils/coreutils-8.19.tar.xz
+ tar -xJf coreutils-8.19.tar.xz
+ cd coreutils-8.19
+ ./configure --prefix=/INSTALL/PATH
+ make
+ sudo make install
+
+
+## AWK
+ wget http://ftp.gnu.org/gnu/gawk/gawk-4.0.1.tar.gz
+ tar -xf gawk-4.0.1.tar.gz
+ cd gawk-4.0.1
+ ./configure --prefix=/INSTALL/PATH
+ make
+ sudo make install
+
+## SED
+ wget ftp://ftp.gnu.org/gnu/sed/sed-4.2.tar.gz
+ wget http://cancan.cshl.edu/labmembers/gordon/files/sed-4.2-sandbox.patch
+ tar -xf sed-4.2.tar.gz
+ patch -p0 < sed-4.2-sandbox.patch
+ cd sed-4.2
+ ./configure --prefix=/INSTALL/PATH
+ make
+ sudo make install
+
+## Grep
+ wget ftp://ftp.gnu.org/gnu/grep/grep-2.14.tar.xz
+ tar -xJf grep-2.14.tar.xz
+ cd grep-2.14
+ ./configure --enable-perl-regexp --prefix=/INSTALL/PATH
+ make
+ sudo make install
+
+