|
20
|
1 # WARNING before you start
|
|
|
2 # Install this tool on a private Galaxy ONLY
|
|
|
3 # Please NEVER on a public or production instance
|
|
|
4 # updated august 2014 by John Chilton adding citation support
|
|
|
5 #
|
|
|
6 # updated august 8 2014 to fix bugs reported by Marius van den Beek
|
|
|
7 # please cite the resource at
|
|
|
8 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
|
|
|
9 # if you use this tool in your published work.
|
|
|
10
|
|
|
11 *Short Story*
|
|
|
12
|
|
|
13 This is an unusual Galaxy tool capable of generating new Galaxy tools.
|
|
|
14 It works by exposing *unrestricted* and therefore extremely dangerous scripting
|
|
|
15 to all designated administrators of the host Galaxy server, allowing them to
|
|
|
16 run scripts in R, python, sh and perl over multiple selected input data sets,
|
|
|
17 writing a single new data set as output.
|
|
|
18
|
|
|
19 *Differences between TF2 and the original Tool Factory*
|
|
|
20
|
|
|
21 1. TF2 (this one) allows any number of either fixed or user-editable parameters to be defined
|
|
|
22 for the new tool. If these are editable, the user can change them but otherwise, they are passed
|
|
|
23 as fixed and invisible parameters for each execution. Obviously, there are substantial security
|
|
|
24 implications with editable parameters, but these are always sanitized by Galaxy's inbuilt
|
|
|
25 parameter sanitization so you may need to "unsanitize" characters - eg translate all "__lt__"
|
|
|
26 into "<" for certain parameters where that is needed. Please practise safe toolshed.
|
|
|
27
|
|
|
28 2. Any number of (the same datatype) of input files may be defined.
|
|
|
29
|
|
|
30 These changes substantially complicate the way your supplied script is supplied with
|
|
|
31 all the new and variable parameters. Examples in each scripting language are shown
|
|
|
32 in the tool help
|
|
|
33
|
|
|
34 *Automated outputs in named sections*
|
|
|
35
|
|
|
36 If your script writes to the current directory path, arbitrary mix of (eg)
|
|
|
37 pdfs, tabular analysis results and run logs,the tool factory can optionally
|
|
|
38 auto-generate a linked Html page with separate sections showing a thumbnail
|
|
|
39 grid for all pdfs and the log text, grouping all artifacts sharing a file
|
|
|
40 name and log name prefix::
|
|
|
41
|
|
|
42 eg: if "foo.log" is emitted then *all* other outputs matching foo_* will
|
|
|
43 all be grouped together - eg
|
|
|
44 foo_baz.pdf
|
|
|
45 foo_bar.pdf and
|
|
|
46 foo_zot.xls
|
|
|
47 would all be displayed and linked in the same section with foo.log's contents
|
|
|
48 - to form the "Foo" section of the Html page. Sections appear in alphabetic
|
|
|
49 order and there are no limits on the number of files or sections.
|
|
|
50
|
|
|
51 *Automated generation of new Galaxy tools for installation into any Galaxy*
|
|
|
52
|
|
|
53 Once a script is working correctly, this tool optionally generates a
|
|
|
54 new Galaxy tool, effectively freezing the supplied script into a new,
|
|
|
55 ordinary Galaxy tool that runs it over one or more input files selected by
|
|
|
56 the user. Generated tools are installed via a tool shed by an administrator
|
|
|
57 and work exactly like all other Galaxy tools for your users.
|
|
|
58
|
|
|
59 If you use the Html output option, please ensure that sanitize_all_html is
|
|
|
60 set to False and uncommented in universe_wsgi.ini - it should show::
|
|
|
61
|
|
|
62 # By default, all tool output served as 'text/html' will be sanitized
|
|
|
63 sanitize_all_html = False
|
|
|
64
|
|
|
65 This opens potential security risks and may not be acceptable for public
|
|
|
66 sites where the lack of stylesheets may make Html pages damage onlookers'
|
|
|
67 eyeballs but should still be correct.
|
|
|
68
|
|
|
69
|
|
|
70 *More Detail*
|
|
|
71
|
|
|
72 To use the ToolFactory, you should have prepared a script to paste into a
|
|
|
73 text box, and a small test input example ready to select from your history
|
|
|
74 to test your new script.
|
|
|
75
|
|
|
76 There is an example in each scripting language on the Tool Factory form. You
|
|
|
77 can just cut and paste these to try it out - remember to select the right
|
|
|
78 interpreter please. You'll also need to create a small test data set using
|
|
|
79 the Galaxy history add new data tool.
|
|
|
80
|
|
|
81 If the script fails somehow, use the "redo" button on the tool output in
|
|
|
82 your history to recreate the form complete with broken script. Fix the bug
|
|
|
83 and execute again. Rinse, wash, repeat.
|
|
|
84
|
|
|
85 Once the script runs sucessfully, a new Galaxy tool that runs your script
|
|
|
86 can be generated. Select the "generate" option and supply some help text and
|
|
|
87 names. The new tool will be generated in the form of a new Galaxy datatype
|
|
|
88 - toolshed.gz - as the name suggests, it's an archive ready to upload to a
|
|
|
89 Galaxy ToolShed as a new tool repository.
|
|
|
90
|
|
|
91 Once it's in a ToolShed, it can be installed into any local Galaxy server
|
|
|
92 from the server administrative interface.
|
|
|
93
|
|
|
94 Once the new tool is installed, local users can run it - each time, the script
|
|
|
95 that was supplied when it was built will be executed with the input chosen
|
|
|
96 from the user's history. In other words, the tools you generate with the
|
|
|
97 ToolFactory run just like any other Galaxy tool,but run your script every time.
|
|
|
98
|
|
|
99 Tool factory tools are perfect for workflow components. One input, one output,
|
|
|
100 no variables.
|
|
|
101
|
|
|
102 *To fully and safely exploit the awesome power* of this tool,
|
|
|
103 Galaxy and the ToolShed, you should be a developer installing this
|
|
|
104 tool on a private/personal/scratch local instance where you are an
|
|
|
105 admin_user. Then, if you break it, you get to keep all the pieces see
|
|
|
106 https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
|
|
|
107
|
|
|
108 ** Installation **
|
|
|
109 This is a Galaxy tool. You can install it most conveniently using the
|
|
|
110 administrative "Search and browse tool sheds" link. Find the Galaxy Main
|
|
|
111 toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory
|
|
|
112 repository. Open it and review the code and select the option to install it.
|
|
|
113
|
|
|
114 (
|
|
|
115 If you can't get the tool that way, the xml and py files here need to be
|
|
|
116 copied into a new tools
|
|
|
117 subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry
|
|
|
118 pointing to the xml
|
|
|
119 file - something like::
|
|
|
120
|
|
|
121 <section name="Tool building tools" id="toolbuilders">
|
|
|
122 <tool file="toolfactory/rgToolFactory.xml"/>
|
|
|
123 </section>
|
|
|
124
|
|
|
125 If not already there (I just added it to datatypes_conf.xml.sample),
|
|
|
126 please add:
|
|
|
127 <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary"
|
|
|
128 mimetype="multipart/x-gzip" subclass="True" />
|
|
|
129 to your local data_types_conf.xml.
|
|
|
130 )
|
|
|
131
|
|
|
132 Of course, R, python, perl etc are needed on your path if you want to test
|
|
|
133 scripts using those interpreters. Adding new ones to this tool code should
|
|
|
134 be easy enough. Please make suggestions as bitbucket issues and code. The
|
|
|
135 HTML file code automatically shrinks R's bloated pdfs, and depends on
|
|
|
136 ghostscript. The thumbnails require imagemagick .
|
|
|
137
|
|
|
138 * Restricted execution *
|
|
|
139 The tool factory tool itself will then be usable ONLY by admin users -
|
|
|
140 people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY
|
|
|
141 admin_users can run this tool** Think about it for a moment. If allowed to
|
|
|
142 run any arbitrary script on your Galaxy server, the only thing that would
|
|
|
143 impede a miscreant bent on destroying all your Galaxy data would probably
|
|
|
144 be lack of appropriate technical skills.
|
|
|
145
|
|
|
146 *What it does* This is a tool factory for simple scripts in python, R and
|
|
|
147 perl currently. Functional tests are automatically generated. How cool is that.
|
|
|
148
|
|
|
149 LIMITED to simple scripts that read one input from the history. Optionally can
|
|
|
150 write one new history dataset, and optionally collect any number of outputs
|
|
|
151 into links on an autogenerated HTML index page for the user to navigate -
|
|
|
152 useful if the script writes images and output files - pdf outputs are shown
|
|
|
153 as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and
|
|
|
154 imagemagik need to be available.
|
|
|
155
|
|
|
156 Generated tools can be edited and enhanced like any Galaxy tool, so start
|
|
|
157 small and build up since a generated script gets you a serious leg up to a
|
|
|
158 more complex one.
|
|
|
159
|
|
|
160 *What you do* You paste and run your script, you fix the syntax errors and
|
|
|
161 eventually it runs. You can use the redo button and edit the script before
|
|
|
162 trying to rerun it as you debug - it works pretty well.
|
|
|
163
|
|
|
164 Once the script works on some test data, you can generate a toolshed compatible
|
|
|
165 gzip file containing your script ready to run as an ordinary Galaxy tool in
|
|
|
166 a repository on your local toolshed. That means safe and largely automated
|
|
|
167 installation in any production Galaxy configured to use your toolshed.
|
|
|
168
|
|
|
169 *Generated tool Security* Once you install a generated tool, it's just
|
|
|
170 another tool - assuming the script is safe. They just run normally and their
|
|
|
171 user cannot do anything unusually insecure but please, practice safe toolshed.
|
|
|
172 Read the fucking code before you install any tool. Especially this one -
|
|
|
173 it is really scary.
|
|
|
174
|
|
|
175 If you opt for an HTML output, you get all the script outputs arranged
|
|
|
176 as a single Html history item - all output files are linked, thumbnails for
|
|
|
177 all the pdfs. Ugly but really inexpensive.
|
|
|
178
|
|
|
179 Patches and suggestions welcome as bitbucket issues please?
|
|
|
180
|
|
|
181 copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
|
|
|
182
|
|
|
183 all rights reserved
|
|
|
184 Licensed under the LGPL if you want to improve it, feel free
|
|
|
185 https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
|
|
|
186
|
|
|
187 Material for our more enthusiastic and voracious readers continues below -
|
|
|
188 we salute you.
|
|
|
189
|
|
|
190 **Motivation** Simple transformation, filtering or reporting scripts get
|
|
|
191 written, run and lost every day in most busy labs - even ours where Galaxy is
|
|
|
192 in use. This 'dark script matter' is pervasive and generally not reproducible.
|
|
|
193
|
|
|
194 **Benefits** For our group, this allows Galaxy to fill that important dark
|
|
|
195 script gap - all those "small" bioinformatics tasks. Once a user has a working
|
|
|
196 R (or python or perl) script that does something Galaxy cannot currently do
|
|
|
197 (eg transpose a tabular file) and takes parameters the way Galaxy supplies
|
|
|
198 them (see example below), they:
|
|
|
199
|
|
|
200 1. Install the tool factory on a personal private instance
|
|
|
201
|
|
|
202 2. Upload a small test data set
|
|
|
203
|
|
|
204 3. Paste the script into the 'script' text box and iteratively run the
|
|
|
205 insecure tool on test data until it works right - there is absolutely no
|
|
|
206 reason to do this anywhere other than on a personal private instance.
|
|
|
207
|
|
|
208 4. Once it works right, set the 'Generate toolshed gzip' option and run
|
|
|
209 it again.
|
|
|
210
|
|
|
211 5. A toolshed style gzip appears ready to upload and install like any other
|
|
|
212 Toolshed entry.
|
|
|
213
|
|
|
214 6. Upload the new tool to the toolshed
|
|
|
215
|
|
|
216 7. Ask the local admin to check the new tool to confirm it's not evil and
|
|
|
217 install it in the local production galaxy
|
|
|
218
|
|
|
219 **Simple examples on the tool form**
|
|
|
220
|
|
|
221 A simple Rscript "filter" showing how the command line parameters can be
|
|
|
222 handled, takes an input file, does something (transpose in this case) and
|
|
|
223 writes the results to a new tabular file::
|
|
|
224
|
|
|
225 # transpose a tabular input file and write as a tabular output file
|
|
|
226 ourargs = commandArgs(TRUE)
|
|
|
227 inf = ourargs[1]
|
|
|
228 outf = ourargs[2]
|
|
|
229 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
|
|
|
230 outp = t(inp)
|
|
|
231 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
|
|
|
232
|
|
|
233 Calculate a multiple test adjusted p value from a column of p values -
|
|
|
234 for this script to be useful, it needs the right column for the input to be
|
|
|
235 specified in the code for the given input file type(s) specified when the
|
|
|
236 tool is generated ::
|
|
|
237
|
|
|
238 # use p.adjust - assumes a HEADER row and column 1 - please fix for any
|
|
|
239 real use
|
|
|
240 column = 1 # adjust if necessary for some other kind of input
|
|
|
241 fdrmeth = 'BH'
|
|
|
242 ourargs = commandArgs(TRUE)
|
|
|
243 inf = ourargs[1]
|
|
|
244 outf = ourargs[2]
|
|
|
245 inp = read.table(inf,head=T,row.names=NULL,sep='\t')
|
|
|
246 p = inp[,column]
|
|
|
247 q = p.adjust(p,method=fdrmeth)
|
|
|
248 newval = paste(fdrmeth,'p-value',sep='_')
|
|
|
249 q = data.frame(q)
|
|
|
250 names(q) = newval
|
|
|
251 outp = cbind(inp,newval=q)
|
|
|
252 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
|
|
|
253
|
|
|
254
|
|
|
255
|
|
|
256 Another Rscript example without any input file - generates a random heatmap
|
|
|
257 pdf - you must make sure the option to create an HTML output file is
|
|
|
258 turned on for this to work. The heatmap will be presented as a thumbnail
|
|
|
259 linked to the pdf in the resulting HTML page::
|
|
|
260
|
|
|
261 # note this script takes NO input or output because it generates random data
|
|
|
262 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),
|
|
|
263 e=runif(100),f=runif(100))
|
|
|
264 bar = as.matrix(foo)
|
|
|
265 pdf( "heattest.pdf" )
|
|
|
266 heatmap(bar,main='Random Heatmap')
|
|
|
267 dev.off()
|
|
|
268
|
|
|
269 A Python example that reverses each row of a tabular file. You'll need
|
|
|
270 to remove the leading spaces for this to work if cut and pasted into the
|
|
|
271 script box. Note that you can already do this in Galaxy by setting up the
|
|
|
272 cut columns tool with the correct number of columns in reverse order,but
|
|
|
273 this script will work for any number of columns so is completely generic::
|
|
|
274
|
|
|
275 # reverse order of columns in a tabular file
|
|
|
276 import sys
|
|
|
277 inp = sys.argv[1]
|
|
|
278 outp = sys.argv[2]
|
|
|
279 i = open(inp,'r')
|
|
|
280 o = open(outp,'w')
|
|
|
281 for row in i:
|
|
|
282 rs = row.rstrip().split('\t')
|
|
|
283 rs.reverse()
|
|
|
284 o.write('\t'.join(rs))
|
|
|
285 o.write('\n')
|
|
|
286 i.close()
|
|
|
287 o.close()
|
|
|
288
|
|
|
289
|
|
|
290 Galaxy as an IDE for developing API scripts
|
|
|
291 If you need to develop Galaxy API scripts and you like to live dangerously,
|
|
|
292 please read on.
|
|
|
293
|
|
|
294 Galaxy as an IDE?
|
|
|
295 Amazingly enough, blend-lib API scripts run perfectly well *inside*
|
|
|
296 Galaxy when pasted into a Tool Factory form. No need to generate a new
|
|
|
297 tool. Galaxy+Tool_Factory = IDE I think we need a new t-shirt. Seriously,
|
|
|
298 it is actually quite useable.
|
|
|
299
|
|
|
300 Why bother - what's wrong with Eclipse
|
|
|
301 Nothing. But, compared with developing API scripts in the usual way outside
|
|
|
302 Galaxy, you get persistence and other framework benefits plus at absolutely
|
|
|
303 no extra charge, a ginormous security problem if you share the history or
|
|
|
304 any outputs because they contain the api script with key so development
|
|
|
305 servers only please!
|
|
|
306
|
|
|
307 Workflow
|
|
|
308 Fire up the Tool Factory in Galaxy.
|
|
|
309
|
|
|
310 Leave the input box empty, set the interpreter to python, paste and run an
|
|
|
311 api script - eg working example (substitute the url and key) below.
|
|
|
312
|
|
|
313 It took me a few iterations to develop the example below because I know
|
|
|
314 almost nothing about the API. I started with very simple code from one of the
|
|
|
315 samples and after each run, the (edited..) api script is conveniently recreated
|
|
|
316 using the redo button on the history output item. So each successive version
|
|
|
317 of the developing api script you run is persisted - ready to be edited and
|
|
|
318 rerun easily. It is ''very'' handy to be able to add a line of code to the
|
|
|
319 script and run it, then view the output to (eg) inspect dicts returned by
|
|
|
320 API calls to help move progressively deeper iteratively.
|
|
|
321
|
|
|
322 Give the below a whirl on a private clone (install the tool factory from
|
|
|
323 the main toolshed) and try adding complexity with few rerun/edit/rerun cycles.
|
|
|
324
|
|
|
325 Eg tool factory api script
|
|
|
326 import sys
|
|
|
327 from blend.galaxy import GalaxyInstance
|
|
|
328 ourGal = 'http://x.x.x.x:xxxx'
|
|
|
329 ourKey = 'xxx'
|
|
|
330 gi = GalaxyInstance(ourGal, key=ourKey)
|
|
|
331 libs = gi.libraries.get_libraries()
|
|
|
332 res = []
|
|
|
333 # libs looks like
|
|
|
334 # u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id':
|
|
|
335 u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data',
|
|
|
336 for lib in libs:
|
|
|
337 res.append('%s:\n' % lib['name'])
|
|
|
338 res.append(str(gi.libraries.show_library(lib['id'],contents=True)))
|
|
|
339 outf=open(sys.argv[2],'w')
|
|
|
340 outf.write('\n'.join(res))
|
|
|
341 outf.close()
|
|
|
342
|
|
|
343 **Attribution**
|
|
|
344 Creating re-usable tools from scripts: The Galaxy Tool Factory
|
|
|
345 Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
|
|
|
346 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
|
|
|
347
|
|
|
348 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
|
|
|
349
|
|
|
350 **Licensing**
|
|
|
351 Copyright Ross Lazarus 2010
|
|
|
352 ross lazarus at g mail period com
|
|
|
353
|
|
|
354 All rights reserved.
|
|
|
355
|
|
|
356 Licensed under the LGPL
|
|
|
357
|
|
|
358 **Obligatory screenshot**
|
|
|
359
|
|
|
360 http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
|
|
|
361
|
