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