Mercurial > repos > bgruening > text_processing
diff readme.rst @ 3:7068d1548234 draft
Uploaded
author | bgruening |
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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. +