# HG changeset patch
# User ross lazarus ross.lazarus@gmail.com
# Date 1338420918 -36000
# Node ID d95513e50c9213db3d463e0ddee5e50fbe6f0b94
# Parent  0133b97e477e032cf7cb3c8a6ea458eddf572a38
Add README.txt for bitbucket

diff -r 0133b97e477e -r d95513e50c92 README.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt	Thu May 31 09:35:18 2012 +1000
@@ -0,0 +1,20 @@
+Motivation: Simple transformation, filtering or reporting scripts get written, run and lost every day in most busy labs - even ours where Galaxy is in use. This 'dark script matter' runs outside Galaxy and without manual effort to curate is often not reproducable.
+
+ After a lot of nagging about how hard it was to create new wrappers for trivial scripts, I wrote a new Galaxy tool (see the source tab) locked down to allow only two other trusted bioinformatician users to paste and run (NO sandbox!) arbitrary scripts - see screenshot attached. Note that this tool allows unrestricted access as user Galaxy so should be restricted to admin users who could run rm -rf from a command line if they wanted to but can be trusted not to! 
+
+For our group, this allows Galaxy to fill that important gap - all those "small" bioinformatics tasks - because once a trusted user has a working R (or python or perl) script that takes parameters the way Galaxy supplies them (see example below), they: 
+
+1) run the new tool
+
+2) paste their code into the tool 'script' text box
+
+3) select the optional history input (and some other odds and ends - see screen shot) and 
+
+4) run the tool and thus the script. 
+
+Rerunning the output reruns the same script of course, so we're now better off than we were before. But what about adding some code to this script runner tool to generate a new Galaxy tool as a ready to install toolshed entry? This (imho) will be a very low impedence way to generate new simple Galaxy tools - run them until they work then package them up and deploy/distribute for any user to use. The tool generator itself is dangerous but it could easily create normal Galaxy tools with no new security risks - in the local toolshed!
+
+That's the goal of this project.
+If this seem like a good idea to anyone else, please join in. First ticket - add a tool repository entry generator - is open and waiting...
+
+http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png is a proof of concept screengrab