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Updated R targets to use r-package build-type.

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commit 17ab0e8bc45f0b2cbb325b32e39aeddada9909df 1 parent a3b7213
Jai Ram Rideout authored March 18, 2013
43  OPTIONS
@@ -34,6 +34,14 @@ Configuration file options:
34 34
                      [python] application section or simply attempt to use
35 35
                      'python' found in the user's PATH.
36 36
 
  37
+    r-exe
  38
+        Supported values: full path to an R executable
  39
+        Description: This R executable will be used for any
  40
+                     r-package applications to build via install.packages(). If
  41
+                     none is specified qiime-deploy will default to bin/R of an
  42
+                     [r] application section or simply attempt to use 'R' found
  43
+                     in the user's PATH.
  44
+
37 45
     append-environment-to-bashrc:
38 46
         Supported values: yes, no
39 47
         Default value: no
@@ -89,7 +97,7 @@ Configuration file options:
89 97
 
90 98
     build-type [REQUIRED]
91 99
         Supported values:  autoconf, python-distutils, make, make-install, 
92  
-                           c-file, cpp-file, ant, copy, custom
  100
+                           c-file, cpp-file, ant, r-package, copy, custom
93 101
         Description: The build type for the application.
94 102
 
95 103
             autoconf: This is the standard GNU autoconf process (./configure;
@@ -138,6 +146,20 @@ Configuration file options:
138 146
     
139 147
             ant: This simply runs 'ant' in the applications base directory.
140 148
 
  149
+            r-package: This runs R's install.packages() function to obtain the
  150
+                       latest version of the package. The package will be
  151
+                       deployed using whichever R qiime-deploy defaults to
  152
+                       (e.g. either via the r-exe setting, deploying an [r]
  153
+                       application as part of the qiime-deploy process,
  154
+                       or as a last case the 'R' in the user's PATH). Requires
  155
+                       that r-package-name and r-package-repo are provided.
  156
+                       Will ignore the following options: release-file-name,
  157
+                       release-location, repository-type, repository-location,
  158
+                       repository-local-name, repository-options,
  159
+                       unzipped-name, skip-unzipped-name, and
  160
+                       copy-source-to-final-deploy (in addition to other build-
  161
+                       type-specific options).
  162
+
141 163
             copy: This simply unzips (if needed) and copies the downloaed
142 164
                   application to the final deploy directory.
143 165
 
@@ -146,24 +168,24 @@ Configuration file options:
146 168
                     supported applications: denoiser, uclust, r, pyronoise,
147 169
                     ampliconnoise, and dotur.
148 170
 
149  
-    release-file-name [REQUIRED or repository-* must be specified]
  171
+    release-file-name [REQUIRED unless repository-* is specified or r-package build-type]
150 172
         Description: This is the name of the file that will be downloaded from
151 173
                      release-location. Note: it will NOT be renamed to this.
152 174
                      release-file-name must match the name from
153 175
                      release-location.
154 176
 
155  
-    release-location [REQUIRED or repository-* must be specified]
  177
+    release-location [REQUIRED unless repository-* is specified or r-package build-type]
156 178
         Description: This is the location of the file to be downloaded. It must
157 179
                      be a single download location.
158 180
 
159  
-    repository-type [REQUIRED or release-* must be specified]
  181
+    repository-type [REQUIRED unless release-* is specified or r-package build-type]
160 182
         Description: The type of repository to checkout from. Currently
161 183
                      subversion (svn co) and git (git clone) are supported.
162 184
 
163  
-    repository-location [REQUIRED or release-* must be specified]
  185
+    repository-location [REQUIRED unless release-* is specified or r-package build-type]
164 186
         Description: Location of the repository to checkout the application.
165 187
 
166  
-    repository-local-name [REQUIRED or release-* must be specified]
  188
+    repository-local-name [REQUIRED unless release-* is specified or r-package build-type]
167 189
         Description: The name of the local directory that the repository should
168 190
                      be placed in.
169 191
 
@@ -235,6 +257,15 @@ Configuration file options:
235 257
         Description: The name of the exe to be generated by either the c-file
236 258
                      or cpp-file build-types.
237 259
 
  260
+    r-package-name
  261
+        Description: The name of the R package to be installed. REQUIRED if
  262
+                     build-type is r-package.
  263
+
  264
+    r-package-repo
  265
+        Description: URL of the R package repository to download the
  266
+                     r-package-name package from. REQUIRED if build-type is
  267
+                     r-package.
  268
+
238 269
     post-bash-commands
239 270
         Description: Any additional bash commands to execute after the entire
240 271
                      build process is complete and successful.
9  picrust-0.9.0-dev/picrust.conf
@@ -78,8 +78,15 @@ set-environment-variables-deploypath: PYCOGENT=./
78 78
 
79 79
 [r]
80 80
 version: 2.12.0
81  
-build-type: custom
  81
+build-type: autoconf
82 82
 release-file-name: R-2.12.0.tar.gz
83 83
 release-location: http://cran.case.edu/src/base/R-2/R-2.12.0.tar.gz
84 84
 relative-directory-add-to-path: bin
85 85
 autoconf-make-options: -j4
  86
+
  87
+[ape]
  88
+version: latest
  89
+build-type: r-package
  90
+r-package-name: ape
  91
+r-package-repo: http://cran.r-project.org
  92
+deps: r
58  qiime-1.5.0/qiime.conf
@@ -227,12 +227,68 @@ relative-directory-add-to-path: .
227 227
 
228 228
 [r]
229 229
 version: 2.12.0
230  
-build-type: custom
  230
+build-type: autoconf
231 231
 release-file-name: R-2.12.0.tar.gz
232 232
 release-location: http://cran.case.edu/src/base/R-2/R-2.12.0.tar.gz
233 233
 relative-directory-add-to-path: bin
234 234
 autoconf-make-options: -j4
235 235
 
  236
+[random-forest]
  237
+version: latest
  238
+build-type: r-package
  239
+r-package-name: randomForest
  240
+r-package-repo: http://cran.r-project.org
  241
+deps: r
  242
+
  243
+[optparse]
  244
+version: latest
  245
+build-type: r-package
  246
+r-package-name: optparse
  247
+r-package-repo: http://cran.r-project.org
  248
+deps: r
  249
+
  250
+[vegan]
  251
+version: latest
  252
+build-type: r-package
  253
+r-package-name: vegan
  254
+r-package-repo: http://cran.r-project.org
  255
+deps: r
  256
+
  257
+[ape]
  258
+version: latest
  259
+build-type: r-package
  260
+r-package-name: ape
  261
+r-package-repo: http://cran.r-project.org
  262
+deps: r
  263
+
  264
+[mass]
  265
+version: latest
  266
+build-type: r-package
  267
+r-package-name: MASS
  268
+r-package-repo: http://cran.r-project.org
  269
+deps: r
  270
+
  271
+[gtools]
  272
+version: latest
  273
+build-type: r-package
  274
+r-package-name: gtools
  275
+r-package-repo: http://cran.r-project.org
  276
+deps: r
  277
+
  278
+[klar]
  279
+version: latest
  280
+build-type: r-package
  281
+r-package-name: klaR
  282
+r-package-repo: http://cran.r-project.org
  283
+deps: r
  284
+
  285
+[r-color-brewer]
  286
+version: latest
  287
+build-type: r-package
  288
+r-package-name: RColorBrewer
  289
+r-package-repo: http://cran.r-project.org
  290
+deps: r
  291
+
236 292
 [ampliconnoise]
237 293
 version: 1.25
238 294
 build-type: custom
58  qiime-1.6.0-dev/qiime.conf
@@ -244,12 +244,68 @@ relative-directory-add-to-path: .
244 244
 
245 245
 [r]
246 246
 version: 2.12.0
247  
-build-type: custom
  247
+build-type: autoconf
248 248
 release-file-name: R-2.12.0.tar.gz
249 249
 release-location: http://cran.case.edu/src/base/R-2/R-2.12.0.tar.gz
250 250
 relative-directory-add-to-path: bin
251 251
 autoconf-make-options: -j4
252 252
 
  253
+[random-forest]
  254
+version: latest
  255
+build-type: r-package
  256
+r-package-name: randomForest
  257
+r-package-repo: http://cran.r-project.org
  258
+deps: r
  259
+
  260
+[optparse]
  261
+version: latest
  262
+build-type: r-package
  263
+r-package-name: optparse
  264
+r-package-repo: http://cran.r-project.org
  265
+deps: r
  266
+
  267
+[vegan]
  268
+version: latest
  269
+build-type: r-package
  270
+r-package-name: vegan
  271
+r-package-repo: http://cran.r-project.org
  272
+deps: r
  273
+
  274
+[ape]
  275
+version: latest
  276
+build-type: r-package
  277
+r-package-name: ape
  278
+r-package-repo: http://cran.r-project.org
  279
+deps: r
  280
+
  281
+[mass]
  282
+version: latest
  283
+build-type: r-package
  284
+r-package-name: MASS
  285
+r-package-repo: http://cran.r-project.org
  286
+deps: r
  287
+
  288
+[gtools]
  289
+version: latest
  290
+build-type: r-package
  291
+r-package-name: gtools
  292
+r-package-repo: http://cran.r-project.org
  293
+deps: r
  294
+
  295
+[klar]
  296
+version: latest
  297
+build-type: r-package
  298
+r-package-name: klaR
  299
+r-package-repo: http://cran.r-project.org
  300
+deps: r
  301
+
  302
+[r-color-brewer]
  303
+version: latest
  304
+build-type: r-package
  305
+r-package-name: RColorBrewer
  306
+r-package-repo: http://cran.r-project.org
  307
+deps: r
  308
+
253 309
 [ampliconnoise]
254 310
 version: 1.27
255 311
 build-type: custom
58  qiime-1.6.0/qiime.conf
@@ -243,12 +243,68 @@ relative-directory-add-to-path: .
243 243
 
244 244
 [r]
245 245
 version: 2.12.0
246  
-build-type: custom
  246
+build-type: autoconf
247 247
 release-file-name: R-2.12.0.tar.gz
248 248
 release-location: http://cran.case.edu/src/base/R-2/R-2.12.0.tar.gz
249 249
 relative-directory-add-to-path: bin
250 250
 autoconf-make-options: -j4
251 251
 
  252
+[random-forest]
  253
+version: latest
  254
+build-type: r-package
  255
+r-package-name: randomForest
  256
+r-package-repo: http://cran.r-project.org
  257
+deps: r
  258
+
  259
+[optparse]
  260
+version: latest
  261
+build-type: r-package
  262
+r-package-name: optparse
  263
+r-package-repo: http://cran.r-project.org
  264
+deps: r
  265
+
  266
+[vegan]
  267
+version: latest
  268
+build-type: r-package
  269
+r-package-name: vegan
  270
+r-package-repo: http://cran.r-project.org
  271
+deps: r
  272
+
  273
+[ape]
  274
+version: latest
  275
+build-type: r-package
  276
+r-package-name: ape
  277
+r-package-repo: http://cran.r-project.org
  278
+deps: r
  279
+
  280
+[mass]
  281
+version: latest
  282
+build-type: r-package
  283
+r-package-name: MASS
  284
+r-package-repo: http://cran.r-project.org
  285
+deps: r
  286
+
  287
+[gtools]
  288
+version: latest
  289
+build-type: r-package
  290
+r-package-name: gtools
  291
+r-package-repo: http://cran.r-project.org
  292
+deps: r
  293
+
  294
+[klar]
  295
+version: latest
  296
+build-type: r-package
  297
+r-package-name: klaR
  298
+r-package-repo: http://cran.r-project.org
  299
+deps: r
  300
+
  301
+[r-color-brewer]
  302
+version: latest
  303
+build-type: r-package
  304
+r-package-name: RColorBrewer
  305
+r-package-repo: http://cran.r-project.org
  306
+deps: r
  307
+
252 308
 [ampliconnoise]
253 309
 version: 1.27
254 310
 build-type: custom

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