diff readme.rst @ 3:7068d1548234 draft

Uploaded
author bgruening
date Sun, 06 Oct 2013 08:22:36 -0400
parents fc862d5bccaf
children 56e80527c482
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--- a/readme.rst	Thu Sep 05 12:42:48 2013 -0400
+++ b/readme.rst	Sun Oct 06 08:22:36 2013 -0400
@@ -1,17 +1,18 @@
-These are Galaxy wrappers for common unix text-processing tools
-===============================================================
+Galaxy wrappers for common unix text-processing tools
+=====================================================
 
 The initial work was done by Assaf Gordon and Greg Hannon's lab ( http://hannonlab.cshl.edu ) 
 in Cold Spring Harbor Laboratory ( http://www.cshl.edu ).
 
 
-The tools are:
+Tools:
 
 * 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/ )
 * sort_columns - Sorting every line according to there columns
 * 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
@@ -37,7 +38,7 @@
 3. SED version 4.2 *with* a special patch
 4. Grep with PCRE support
 
-These will be installed automatically with the Galaxy Tool Shed.
+These will be installed automatically with the Galaxy `Tool Shed`_.
 
 
 -------------------
@@ -50,22 +51,29 @@
 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 try fix them.
 
 ------------
 Installation
 ------------
 
-Should be done with the Galaxy `Tool Shed`_.
+Should be done via the Galaxy `Tool Shed`_.
 
 .. _`Tool Shed`: http://wiki.galaxyproject.org/Tool%20Shed
 
@@ -84,6 +92,30 @@
 - evaluate the join wrappers against the Galaxy ones, maybe we should drop them
 
 
+-------
+License
+-------
+
+* Copyright (c) 2009-2013   A. Gordon  (gordon <at> cshl dot edu)
+* Copyright (c) 2013   B. Gruening  (bjoern dot gruening <at> gmail dot com)
 
 
+Permission is hereby granted, free of charge, to any person obtaining 
+a copy of this software and associated documentation files (the 
+"Software"), to deal in the Software without restriction, including 
+without limitation the rights to use, copy, modify, merge, publish, 
+distribute, sublicense, and/or sell copies of the Software, and to 
+permit persons to whom the Software is furnished to do so, subject to 
+the following conditions:
 
+The above copyright notice and this permission notice shall be 
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY 
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 
+