Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin
changeset 18:943d4f0ee7c1
More better doco
| author | ross lazarus ross.lazarus@gmail.com |
|---|---|
| date | Mon, 04 Jun 2012 21:32:24 +1000 |
| parents | 187c8b023595 |
| children | a87a262220a4 |
| files | README.txt |
| diffstat | 1 files changed, 20 insertions(+), 48 deletions(-) [+] |
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--- a/README.txt Mon Jun 04 20:59:46 2012 +1000 +++ b/README.txt Mon Jun 04 21:32:24 2012 +1000 @@ -1,39 +1,43 @@ ## 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 +# To fully and safely exploit the awesome power of Galaxy with this tool installed +# you should be a developer installing this tool on a +# personal/scratch local instance - ie a private site +# because then, if you break it, you get to keep all the pieces +# see 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. +# 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! +# Generated tools can be edited and enhanced like any Galaxy tool, so start small and build up +# A generated script gets you a serious leg up to a more complex one. # # 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 +# you fix the syntax errors and eventually it runs +# that's kind of cool, but +# now things get even more interesting. +# Once the script works 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. - +# containing your script neatly wrapped as an ordinary Galaxy script in your +# local toolshed forsafe and largely automated installation in a production Galaxy. +# tests are being worked on - should be done soon +# # 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 +# Read the fucking code before you install any tool. +# Especially this one - it is really scary. # 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. +# Patches welcome 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: @@ -42,8 +46,6 @@ # 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. @@ -79,37 +81,7 @@ 7. Ask the local admin to check the new tool to confirm it's not evil and install it in the local production galaxy -**What it does** This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy. -New mantra: Galaxy can efficiently soak up all your lab's dark script matter and make it reproducible and shareable. - - -**Input options** This version is limited to simple transformation or reporting requiring only a single input file selected from the history. - -**Output options** Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs, -a new HTML report linking all the files and images created by the script can be automatically generated. - -**Tool Generation option** Once the script is working with test data, this tool will optionally generate a new Galaxy tool -in a gzip file ready to upload to your local toolshed for sharing and installation. - -**Permission to to use this tool** must be explicitly granted by an administrator adding approved Galaxy user IDs to the local tool XML list -of permitted users. *It will not run otherwise* - -**Note to system administrators** This tool offers *NO* built in protection against malicious scripts and should only be installed on private/personal -Galaxy instances. Under no circumstances should you allow any user to use this tool unless you trust them with the power to do what they want -as the Galaxy user. - -The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always -be checked carefully before installation. - -**Use on public servers** is STRONGLY discouraged for obvious reasons - -**Scripting conventions** The pasted script will be executed with the path to the (optional) input tabular data file path or NONE if you do not -select one, and the path to the optional output file or None if none is wanted, as the first and second command line parameters. The script must -deal appropriately with these - see Rscript examples below. Note that if an optional HTML output is selected, all the output files created by -the script will be nicely presented as links, with pdf images linked as thumbnails in that output. -This can be handy for complex scripts creating lots of output. - -**Simple examples** +**Simple examples on the tool form** A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and writes the results to a new tabular file::