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# WARNING before you start Install this tool on a private Galaxy ONLY Please NEVER 
# on a public or production instance

Please cite: 
http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref 
if you use this tool in your published work.

*Short Story*

This is an unusual Galaxy tool that exposes unrestricted and therefore extremely 
dangerous scripting to designated administrative users of a Galaxy server, 
allowing them to run scripts in R, python, sh and perl over a single input data 
set, writing a single new data set as output.

In addition, this tool optionally generates very simple new Galaxy tools, that 
effectively freeze the supplied script into a new, ordinary Galaxy tool that runs 
it over a single input file, working just like any other Galaxy tool for your 
users.

To use the ToolFactory, you should have prepared a script to paste into a text 
box, and a small test input example ready to select from your history to test your 
new script. There is an example in each scripting language on the Tool Factory 
form. You can just cut and paste these to try it out - remember to select the 
right interpreter please. You'll also need to create a small test data set using 
the Galaxy history add new data tool.

If the script fails somehow, use the "redo" button on the tool output in your 
history to recreate the form complete with broken script. Fix the bug and execute 
again. Rinse, wash, repeat.

Once the script runs sucessfully, a new Galaxy tool that runs your script can be 
generated. Select the "generate" option and supply some help text and names. The 
new tool will be generated in the form of a new Galaxy datatype - toolshed.gz - as 
the name suggests, it's an archive ready to upload to a Galaxy ToolShed as a new 
tool repository. 

In fact, it's simply a gzip'd mercurial repository. You can modify the code
and (eg) add additional parameters or I/O. The archive can still be used to 
create or update a toolshed repository after you edit and freshen it.

Once it's in a ToolShed, it can be installed into any local Galaxy server from the 
server administrative interface.

Once the new tool is installed, local users can run it - each time, the script 
that was supplied when it was built will be executed with the input chosen from 
the user's history. In other words, the tools you generate with the ToolFactory 
run just like any other Galaxy tool, but run your script every time.

Tool factory tools are perfect for workflow components. One input, one output, no 
variables.

*Reasons to read further*

If you use Galaxy to support your research;

You and fellow users are sometimes forced to take data out of Galaxy, process it 
with ugly little perl/awk/sed/R... scripts and put it back;

You do this when you can't do some transformation in Galaxy (the 90/10 rule);

You don't have enough developer resources for wrapping dozens of even relatively 
simple tools;

Your research and your institution would be far better off if those feral scripts 
were all tucked safely in your local toolshed and Galaxy histories.

*The good news* If it can be trivially scripted, it can be running safely in your 
local Galaxy via your own local toolshed in a few minutes - with functional tests.


*Value proposition* The ToolFactory allows Galaxy to efficiently take over most of 
your lab's dark script matter, making it reproducible in Galaxy and shareable 
through the ToolShed.

That's what this tool does. You paste a simple script and the tool returns a new, 
real Galaxy tool, ready to be installed from the local toolshed to local servers. 
Scripts can be wrapped and online literally within minutes.

*To fully and safely exploit the awesome power* of this tool, Galaxy and the 
ToolShed, you should be a developer installing this tool on a 
private/personal/scratch local instance where you are an admin_user. Then, if you 
break it, you get to keep all the pieces see 
https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home

** Installation ** This is a Galaxy tool. You can install it most conveniently 
using the administrative "Search and browse tool sheds" link. Find the Galaxy Test 
toolshed (not main) and search for the toolfactory repository. Open it and review 
the code and select the option to install it.

If you can't get the tool that way, the xml and py files here need to be copied 
into a new tools subdirectory such as tools/toolfactory Your tool_conf.xml needs a 
new entry pointing to the xml file - something like::

  <section name="Tool building tools" id="toolbuilders">
    <tool file="toolfactory/rgToolFactory.xml"/>
  </section>

If not already there (I just added it to datatypes_conf.xml.sample), please add: 
<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" 
mimetype="multipart/x-gzip" subclass="True" /> to your local data_types_conf.xml.

Ensure that html sanitization is set to False and uncommented in universe_wsgi.ini

You'll have to restart the server for the new tool to be available.

Of course, R, python, perl etc are needed on your path if you want to test scripts 
using those interpreters. Adding new ones to this tool code should be easy enough. 
Please make suggestions as bitbucket issues and code. The HTML file code 
automatically shrinks R's bloated pdfs, and depends on ghostscript. The thumbnails 
require imagemagick .

* Restricted execution * The new tool factory tool will then be usable ONLY by 
admin users - people with IDs in admin_users in universe_wsgi.ini **Yes, that's 
right. ONLY admin_users can run this tool** Think about it for a moment. If 
allowed to run any arbitrary script on your Galaxy server, the only thing that 
would impede a miscreant bent on destroying all your Galaxy data would probably be 
lack of appropriate technical skills.

*What it does* This is a tool factory for simple scripts in python, R and perl 
currently. Functional tests are automatically generated. How cool is that.

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 index page for the user to navigate - useful if the 
script writes images and output files - pdf outputs are shown as thumbnails and 
R's bloated pdf's are shrunk with ghostscript so that and imagemagik need to be 
avaailable.

Generated tools can be edited and enhanced like any Galaxy tool, so start small 
and build up since a generated script gets you a serious leg up to a more complex 
one.

*What you do* You paste and run your script you fix the syntax errors and 
eventually it runs You can use the redo button and edit the script before trying 
to rerun it as you debug - it works pretty well.

Once the script works on some test data, you can generate a toolshed compatible 
gzip file containing your script ready to run as an ordinary Galaxy tool in a 
repository on your local toolshed. That means safe and largely automated 
installation in any production Galaxy configured to use your toolshed.

*Generated tool Security* Once you install a generated tool, it's just another 
tool - assuming 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 - 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 and suggestions welcome as bitbucket issues please?

long route to June 2012 product 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




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 and voracious readers continues below - we 
salute you.

**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.

**Benefits** For our group, this allows Galaxy to fill that important dark script 
gap - all those "small" bioinformatics tasks. Once a user has a working R (or 
python or perl) script that does something Galaxy cannot currently do (eg 
transpose a tabular file) and takes parameters the way Galaxy supplies them (see 
example below), they:

1. Install the tool factory on a personal private instance

2. Upload a small test data set

3. Paste the script into the 'script' text box and iteratively run the insecure 
tool on test data until it works right - there is absolutely no reason to do this 
anywhere other than on a personal private instance.

4. Once it works right, set the 'Generate toolshed gzip' option and run it again.

5. A toolshed style gzip appears ready to upload and install like any other 
Toolshed entry.

6. Upload the new tool to the toolshed

7. Ask the local admin to check the new tool to confirm it's not evil and install 
it in the local production galaxy

**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::

 # transpose a tabular input file and write as a tabular output file
 ourargs = commandArgs(TRUE)
 inf = ourargs[1]
 outf = ourargs[2]
 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
 outp = t(inp)
 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)

Calculate a multiple test adjusted p value from a column of p values - for this 
script to be useful, it needs the right column for the input to be specified in 
the code for the given input file type(s) specified when the tool is generated ::

 # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
 column = 1 # adjust if necessary for some other kind of input
 fdrmeth = 'BH'
 ourargs = commandArgs(TRUE)
 inf = ourargs[1]
 outf = ourargs[2]
 inp = read.table(inf,head=T,row.names=NULL,sep='\t')
 p = inp[,column]
 q = p.adjust(p,method=fdrmeth)
 newval = paste(fdrmeth,'p-value',sep='_')
 q = data.frame(q)
 names(q) = newval
 outp = cbind(inp,newval=q)
 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)



Another Rscript example without any input file - generates a random heatmap pdf - 
you must make sure the option to create an HTML output file is turned on for this 
to work. The heatmap will be presented as a thumbnail linked to the pdf in the 
resulting HTML page::

 # note this script takes NO input or output because it generates random data
 foo = 
data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
 bar = as.matrix(foo)
 pdf( "heattest.pdf" )
 heatmap(bar,main='Random Heatmap')
 dev.off()

A Python example that reverses each row of a tabular file. You'll need to remove 
the leading spaces for this to work if cut and pasted into the script box. Note 
that you can already do this in Galaxy by setting up the cut columns tool with the 
correct number of columns in reverse order,but this script will work for any 
number of columns so is completely generic::

# reverse order of columns in a tabular file
import sys inp = sys.argv[1] outp = sys.argv[2] i = open(inp,'r') o = 
open(outp,'w') for row in i:
    rs = row.rstrip().split('\t')
    rs.reverse()
    o.write('\t'.join(rs))
    o.write('\n') i.close() o.close()


Galaxy as an IDE for developing API scripts If you need to develop Galaxy API 
scripts and you like to live dangerously, please read on.

Galaxy as an IDE? Amazingly enough, blend-lib API scripts run perfectly well 
*inside* Galaxy when pasted into a Tool Factory form. No need to generate a new 
tool. Galaxy+Tool_Factory = IDE I think we need a new t-shirt. Seriously, it is 
actually quite useable.

Why bother - what's wrong with Eclipse Nothing. But, compared with developing API 
scripts in the usual way outside Galaxy, you get persistence and other framework 
benefits plus at absolutely no extra charge, a ginormous security problem if you 
share the history or any outputs because they contain the api script with key so 
development servers only please!

Workflow Fire up the Tool Factory in Galaxy.

Leave the input box empty, set the interpreter to python, paste and run an api 
script - eg working example (substitute the url and key) below.

It took me a few iterations to develop the example below because I know almost 
nothing about the API. I started with very simple code from one of the samples and 
after each run, the (edited..) api script is conveniently recreated using the redo 
button on the history output item. So each successive version of the developing 
api script you run is persisted - ready to be edited and rerun easily. It is 
''very'' handy to be able to add a line of code to the script and run it, then 
view the output to (eg) inspect dicts returned by API calls to help move 
progressively deeper iteratively.

Give the below a whirl on a private clone (install the tool factory from the main 
toolshed) and try adding complexity with few rerun/edit/rerun cycles.

Eg tool factory api script import sys from blend.galaxy import GalaxyInstance 
ourGal = 'http://x.x.x.x:xxxx' ourKey = 'xxx' gi = GalaxyInstance(ourGal, 
key=ourKey) libs = gi.libraries.get_libraries() res = []
# libs looks like u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id': 
# u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data',
for lib in libs:
    res.append('%s:\n' % lib['name'])
    res.append(str(gi.libraries.show_library(lib['id'],contents=True))) 
outf=open(sys.argv[2],'w') outf.write('\n'.join(res)) outf.close()

**Attribution** Creating re-usable tools from scripts: The Galaxy Tool Factory 
Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team Bioinformatics 2012; 
doi: 10.1093/bioinformatics/bts573

http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref

**Licensing** Copyright Ross Lazarus 2010 ross lazarus at g mail period com

All rights reserved.

Licensed under the LGPL

**Obligatory screenshot**

http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png


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