af234763534bdbc3ec7fc59a3f7d56d4672c646c
cli_beta.md
... | ... | @@ -66,6 +66,8 @@ To install the software, you must have valid credentials provided by SBGrid. |
66 | 66 | |
67 | 67 | Activate with the 'activate' subcommand |
68 | 68 | |
69 | +**activate** |
|
70 | + |
|
69 | 71 | ``` |
70 | 72 | Usage: activate [options] [site] [user] [key] |
71 | 73 | |
... | ... | @@ -79,12 +81,29 @@ Options: |
79 | 81 | |
80 | 82 | Trouble activating? See Troubleshooting options further down this page. |
81 | 83 | |
84 | +**reactivate** |
|
85 | + |
|
86 | +*reactivate* can restore from a saved config file. See below. |
|
87 | + |
|
88 | +``` |
|
89 | + $ ./sbgrid reactivate -h |
|
90 | +Usage: reactivate [options] <configFilePath> [packagesPath] |
|
91 | + |
|
92 | +reactivate a new instance of an installation using a “saved” configuration file |
|
93 | +to repair an existing installation see “reinstall --all-versions” |
|
94 | + |
|
95 | +Options: |
|
96 | + --skip-folder-checking skip checking if folder with programs already exists |
|
97 | + --just-activation skip software titles installation |
|
98 | + -h, --help output usage information |
|
99 | +``` |
|
100 | + |
|
82 | 101 | ### Listing available titles, status |
83 | 102 | |
84 | 103 | The *sbgrid list* command will show all available titles. They are normally colored by their installation status. |
85 | 104 | Available options : |
86 | 105 | |
87 | -list |
|
106 | +**list** |
|
88 | 107 | |
89 | 108 | ``` |
90 | 109 | Usage: list [options] [title] [otherTitles...] |
... | ... | @@ -101,14 +120,18 @@ Options: |
101 | 120 | ``` |
102 | 121 | |
103 | 122 | **updates** |
104 | -See available updates |
|
123 | + |
|
124 | +Shows available updated version and titles |
|
105 | 125 | |
106 | 126 | ``` |
107 | 127 | ./sbgrid updates |
108 | 128 | ``` |
109 | 129 | |
110 | 130 | **obsolete** |
111 | -See obsolete versions |
|
131 | + |
|
132 | +Shows obsolete versions that will be removed. |
|
133 | +Obsolete versions are previously installed versions no longer included in the SBGrid installation. |
|
134 | + |
|
112 | 135 | ``` |
113 | 136 | ./sbgrid obsolete |
114 | 137 | ``` |
... | ... | @@ -117,7 +140,7 @@ See obsolete versions |
117 | 140 | |
118 | 141 | **info** |
119 | 142 | |
120 | -Information about each title, including a description and links to documentation can be show with the *sbgrid info <title>* command. See example below. |
|
143 | +The *info* flag shows information about each title, including a description and links to documentation can be show with the *sbgrid info <title>* command. See example below. |
|
121 | 144 | |
122 | 145 | ``` |
123 | 146 | Usage: info [options] [title] [otherTitles...] |
... | ... | @@ -130,7 +153,7 @@ Options: |
130 | 153 | -h, --help output usage information |
131 | 154 | ``` |
132 | 155 | |
133 | -For RELION : |
|
156 | +For example, info for RELION : |
|
134 | 157 | |
135 | 158 | ``` |
136 | 159 | $ ./sbgrid info relion |
... | ... | @@ -202,25 +225,27 @@ Options: |
202 | 225 | -h, --help output usage information |
203 | 226 | ``` |
204 | 227 | |
228 | +**Install examples :** |
|
229 | + |
|
205 | 230 | Install a single default version of an application : |
206 | 231 | |
207 | 232 | ``` |
208 | 233 | ./sbgrid install relion |
209 | 234 | ``` |
210 | 235 | |
211 | -Install a specific version of a title : |
|
236 | +Install a specific version of a relion : |
|
212 | 237 | |
213 | 238 | ``` |
214 | 239 | ./sbgrid install relion@3.0.8 |
215 | 240 | ``` |
216 | 241 | |
217 | -Install all versions of a titles : |
|
242 | +Install all versions of relion : |
|
218 | 243 | |
219 | 244 | ``` |
220 | 245 | ./sbgrid install relion@all |
221 | 246 | ``` |
222 | 247 | |
223 | -Install a collection of titles : |
|
248 | +Install the 'Electron Microscopy' collection of titles (see above *list* command to list *collections*): |
|
224 | 249 | |
225 | 250 | ``` |
226 | 251 | $ ./sbgrid install -c 'Electron Microscopy' |
... | ... | @@ -232,7 +257,7 @@ Install all default versions of all titles : |
232 | 257 | ./sbgrid install --all-defaults |
233 | 258 | ``` |
234 | 259 | |
235 | -Install all versions of all titles : |
|
260 | +Install all versions of all titles ( The full collection): |
|
236 | 261 | |
237 | 262 | ``` |
238 | 263 | ./sbgrid install --all-versions |
... | ... | @@ -240,7 +265,7 @@ Install all versions of all titles : |
240 | 265 | |
241 | 266 | **remove** |
242 | 267 | |
243 | -Same options as install |
|
268 | +Same options as install flag above. |
|
244 | 269 | |
245 | 270 | ``` |
246 | 271 | remove software title(s) |
... | ... | @@ -258,34 +283,82 @@ Options: |
258 | 283 | |
259 | 284 | ### Updating titles |
260 | 285 | |
286 | +Updates are performed when default titles change to a new version or bugs are fixed in existing verisons. To update, use the update flag. |
|
287 | + |
|
261 | 288 | **update** |
262 | 289 | |
263 | 290 | ``` |
264 | 291 | ./sbgrid update relion |
265 | 292 | ``` |
266 | 293 | |
294 | +### Remove obsolete titles |
|
295 | + |
|
296 | +Use the obsolete flag to list or remove obsolete versions or titles |
|
297 | + |
|
298 | +**obsolete** |
|
299 | + |
|
300 | +``` |
|
301 | + $ ./sbgrid obsolete -h |
|
302 | +Usage: obsolete [options] |
|
303 | + |
|
304 | +list obsolete software versions |
|
305 | + |
|
306 | +Options: |
|
307 | + -r, --remove remove the obsolete software versions |
|
308 | + -y, --yes continue without confirmation |
|
309 | + -h, --help output usage information |
|
310 | + ``` |
|
311 | + |
|
267 | 312 | ## Advanced modes |
268 | 313 | |
314 | +The advanced modes perform multiple actions and are designed for automated use for a managed 'rolling release' installation. |
|
315 | + |
|
269 | 316 | **clean** |
270 | 317 | |
271 | 318 | Removes all obsolete software versions and titles |
272 | 319 | |
273 | 320 | **admin** |
274 | 321 | |
275 | -run periodic installation. Install all new, update all and clean up all obsolete versions |
|
322 | +Run periodic installation, update and removal. Installs all new titles, updates where appropriate and cleans up (removes) obsolete versions |
|
323 | + |
|
324 | +``` |
|
325 | +Usage: admin [options] |
|
326 | + |
|
327 | +periodic update and installation |
|
328 | + |
|
329 | +Options: |
|
330 | + -a, --all-versions install all versions of all available software titles |
|
331 | + -r, --reinstall reinstall all of installed software titles |
|
332 | + -h, --help output usage information |
|
333 | +``` |
|
334 | + |
|
335 | +For example running |
|
336 | + |
|
337 | +``` |
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338 | +./sbgrid admin |
|
339 | +``` |
|
340 | + |
|
341 | +will install all default, update all installed titles and remove all obsolete versions while |
|
342 | + |
|
343 | +``` |
|
344 | +./sbgrid admin -a |
|
345 | +``` |
|
346 | + |
|
347 | +will install all versions of all titles, add any new titles, update any pending updates, and remove obsolete versions. |
|
348 | +This |
|
349 | + |
|
276 | 350 | |
277 | 351 | **rebuild** |
278 | 352 | |
279 | -rebuild installation environment |
|
353 | +*rebuild* rebuilds the installation environment configuration files. |
|
280 | 354 | |
281 | 355 | **crontab** |
282 | 356 | |
283 | -Writes a basic script for crontab |
|
284 | - |
|
357 | +Writes a basic script for crontab for *admin* functionality |
|
285 | 358 | |
286 | 359 | **save** |
287 | 360 | |
288 | -save current configuration |
|
361 | +The *save* flag saves the current configuration so it can be restored at a later stage or replicated on another machine (or in the cloud). |
|
289 | 362 | |
290 | 363 | |
291 | 364 | ## Troubleshooting and diagnostics |
... | ... | @@ -299,7 +372,6 @@ troubleshooting and diagnostics |
299 | 372 | **verify** |
300 | 373 | list missing software versions and .rc files |
301 | 374 | |
302 | - |
|
303 | 375 | ### Software Version Management in the SBGrid environment |
304 | 376 | If you have a single version of an application installed, explicit version selection in your environment is not needed. |
305 | 377 | |
... | ... | @@ -330,4 +402,4 @@ or in tcsh |
330 | 402 | |
331 | 403 | * **rsync required on 873 or 8080**. The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available. You can check if you can access [port 873 here](http://portquiz.net:873) and [port 8080 here](http://portquiz.net:8080) |
332 | 404 | |
333 | -For help, email *bugs@sbgrid.org.* |
|
405 | +For help or to report issues, please email *bugs@sbgrid.org.* |