# HG changeset patch # User ross lazarus ross.lazarus@gmail.com # Date 1338807586 -36000 # Node ID 187c8b023595c24dd9b94200e5a4e79ec8004c00 # Parent 36df24947ab322d62ae3b56f6945eea65edf8679 more doco good diff -r 36df24947ab3 -r 187c8b023595 README.txt --- a/README.txt Mon Jun 04 16:22:51 2012 +1000 +++ b/README.txt Mon Jun 04 20:59:46 2012 +1000 @@ -1,5 +1,61 @@ -**WARNING before you start** This tool should only ever be installed on a private Galaxy instance - Please NEVER use it on a public -Galaxy because the risks are too awful to contemplate let alone manage. You have been warned. +## WARNING before you start +## Install on a private Galaxy ONLY +## Please NEVER on a public or production instance +# https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home + +# this is a tool factory for simple scripts in python, R or whatever ails ye. +## LIMITED to simple scripts that read one input from the history. +# Optionally can write one new history dataset, +# and optionally collect any number of outputs into links on an autogenerated HTML page. +## Generated tools can be edited and enhanced like any Galaxy tool, so start small! +# +# you paste and run your script +# you fix the syntax errors and eventually it runs. + +# After you get the script working on some test data, you can +# optionally generate a toolshed compatible gzip file +# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for +# safe and largely automated installation in a production Galaxy. + +# DO NOT install on a public or important site - please. + +# installed generated tools are fine if the script is safe. +# They just run normally and their user cannot do anything unusually insecure +# but please, practice safe toolshed. +# Read the fucking code before you install any tool +# especially this one + +# If you opt for an HTML output, you get all the script outputs arranged +# as a single Html history item - all output files are linked, thumbnails for all the pdfs. +# Ugly but really inexpensive. +# +# Patches appreciated please. +# +# +# long route to June 2012 product +# Behold the awesome power of Galaxy and the toolshed with the tool factory binds to bind them +# derived from an integrated script model +# called rgBaseScriptWrapper.py +# Note to the unwary: +# This tool allows arbitrary scripting on your Galaxy as the Galaxy user +# There is nothing stopping a malicious user doing whatever they choose +# Extremely dangerous!! +# Totally insecure. So, trusted users only +# +# preferred model is a developer using their throw away workstation instance - ie a private site. +# no real risk. +# a list in the xml source file is searched for users permitted to run this tool. +# PUT some IDs in the list in the XML before you restart Galaxy to load this new tool please +# otherwise, the tool won't run for anybody. +# + +# +# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 +# +# all rights reserved +# Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home + +# Material for our more enthusiastic readers continues below **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' is pervasive and generally not reproducible.