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