_Sidebar.md
... ...
@@ -37,5 +37,5 @@ Portals
37 37
* [Data Processing After WSMR](wsmr-worked)
38 38
* [SBGrid SHARP server](sharp)
39 39
40
-Beta
41
-* [SBGrid CLI v2.0 Beta ](cli_beta)
40
+Latest CLI
41
+* [SBGrid CLI v2.0 ](cli_v2)
cli_beta.md
... ...
@@ -1,424 +0,0 @@
1
-## SBGrid command line installation client - v2.0.43
2
-
3
-## How do I get it?
4
-
5
-[LINUX : sbgrid-cli_2.0.43_linux.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.0.43_linux.tar.gz)
6
-
7
-[macOS : sbgrid-cli_2.0.43_macOS.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.0.43_macOS.tar.gz)
8
-
9
-## Supported OSes
10
-[Linux (CentOS/RHEL 7 or 8 recommended) or Apple OSX computers running MacOSX v10.12 - 10.15.](operatingsystems)
11
-
12
-
13
-MacOS 10.15 Catalina can be used, but a work-around is required to add the /programs path.
14
-See [here for more info :](catalina)
15
-
16
-### Pre-installation requirements
17
-**Admin access required on your computer.**
18
- The SBGrid installation client will install the software tree to /opt/sbgrid and create a symlink from this directory to /programs.
19
- While admin privileges are not required to run the application, you will likely need admin privileges to create /opt/sbgrid and /programs .
20
-
21
-```
22
- $ ./sbgrid-cli
23
-Usage: sbgrid-cli [command] [options]
24
-
25
-Commands:
26
- help [command] command-specific help
27
-
28
- activate [options] <site user key> | <credential-key> activate a new installation
29
- reactivate [options] <configFilePath> [packagesPath] reactivate installation using config or package list
30
-
31
- install [options] [title] [otherTitles...] install package(s)
32
- remove|uninstall [options] [title] [otherTitles...] remove package(s)
33
- reinstall [options] [title] [otherTitles...] reinstall package(s)
34
- update|upgrade [options] [title] [otherTitles...] update package(s) to the latest release/version
35
-
36
- list [options] [title] list available software titles
37
- installed list installed software titles
38
- updates list available updates
39
- pending list pending installations
40
- obsolete list obsolete software titles
41
- search <query> search availble titles
42
- collections list available package collections
43
- grids list available software trees
44
- info [options] [title] print title information
45
- shell start SBGrid Shell
46
-
47
- clean [options] remove obsolete software versions and titles
48
- admin [options] run periodic installation, update and clean up
49
- rebuild rebuild installation environment
50
- crontab [options] basic script for crontab
51
- save [filename] save current configuration
52
-
53
- check-connection connectivity checks
54
- diag [options] troubleshooting and diagnostics
55
- verify list missing software versions and .rc files
56
-
57
- Options:
58
- -V, --version version
59
- --verbose verbose output
60
- --quiet disable output
61
- -h, --help usage information
62
- --linux specify linux as platform
63
- --darwin specify macOS as platform
64
- --no-color disable output colors
65
-```
66
-
67
-## General Usage
68
-The SBGrid command line installation client takes subcommands and arguments to those commands to perform various tasks. These can be found in the usage info shown above.
69
-Each subcommand can also take a -h or --help argument to show usage info.
70
-
71
-### Activation
72
-To install the software, you must have valid credentials provided by SBGrid.
73
-
74
-Activate with the 'activate' subcommand
75
-
76
-**activate**
77
-
78
-```
79
-Usage: activate [options] [site] [user] [key]
80
-
81
-activate new installation using credentials provided
82
-(credentials are sent via email and can either be a single credential-key, or a site username key triplet)
83
-
84
-Options:
85
- -k, --credential-key <credential-key> activate with activation key
86
- -h, --help output usage information
87
-```
88
-
89
-Trouble activating? See Troubleshooting options further down this page.
90
-
91
-**reactivate**
92
-
93
-*reactivate* can restore from a saved config file. See below.
94
-
95
-```
96
- $ ./sbgrid-cli reactivate -h
97
-Usage: reactivate [options] <configFilePath> [packagesPath]
98
-
99
-reactivate a new instance of an installation using a “saved” configuration file
100
-to repair an existing installation see “reinstall --all-versions”
101
-
102
-Options:
103
- --skip-folder-checking skip checking if folder with programs already exists
104
- --just-activation skip software titles installation
105
- -h, --help output usage information
106
-```
107
-
108
-### Listing available titles, status
109
-
110
-The *sbgrid list* command will show all available titles. They are normally colored by their installation status.
111
-Available options :
112
-
113
-**list**
114
-
115
-```
116
-Usage: list [options] [title] [otherTitles...]
117
-
118
-list available software titles
119
-
120
-Options:
121
- -a, --all-versions list all available software versions
122
- -d, --default-versions list default software versions
123
- -c, --collections list available collections
124
- -o, --one-column list software in one column
125
- -l, --long-format list software versions in long format
126
- -h, --help output usage information
127
-```
128
-
129
-**updates**
130
-
131
-Shows available updated version and titles
132
-
133
-```
134
-./sbgrid-cli updates
135
-```
136
-
137
-**obsolete**
138
-
139
-Shows obsolete versions that will be removed.
140
-Obsolete versions are previously installed versions no longer included in the SBGrid installation.
141
-
142
-```
143
-./sbgrid-cli obsolete
144
-```
145
-
146
-### Getting Information about titles
147
-
148
-**info**
149
-
150
-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.
151
-
152
-```
153
-Usage: info [options] [title] [otherTitles...]
154
-
155
-print software title(s) metadata
156
-
157
-Options:
158
- -v, --versions list available and default versions for <title> on current platform
159
- -c, --collections list available collections with software count
160
- -h, --help output usage information
161
-```
162
-
163
-For example, info for RELION :
164
-
165
-```
166
- $ ./sbgrid-cli info relion
167
-Fetching requested info...
168
-------------------------------------------------------------------------------------
169
-Package information for relion (i386-mac):
170
-
171
-Package: RELION
172
-Title: relion
173
-Architecture: i386-mac
174
-
175
-Available version(s):
176
- * 1.3 (installed) depends on: openmpi (1.8.4)
177
- * 1.4 (installed) depends on: openmpi (1.8.4)
178
- * 2.1 (installed) depends on: openmpi (2.1.2)
179
- * 3.0.6 (installed) depends on: openmpi (2.1.3)
180
- * 3.0.7 (installed) depends on: openmpi (2.1.3)
181
- * 3.0.8 (installed, default)
182
- * 3.1-beta (installed)
183
-
184
-Grid(s): SBGrid
185
-Collection(s): Electron Microscopy
186
-
187
-Description:
188
-(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
189
-
190
-Technical notes:
191
-**GPU-accelerated RELION : ** RELION versions > 2.0 are GPU-accelerated using Nvidia CUDA on Linux.
192
-For general information on running GPU accelerated applications from SBGrid, please see here : https://sbgrid.org/wiki/gpu</a>
193
-
194
-CUDA builds of RELION are designated by a '_cu<cuda_version>' suffix in the version of the application.
195
-For example, 2.0.4_cu7.5 is linked against CUDA v7.5 libraries and is not recommended for Pascal architecture Nvidia hardware (GTX 1080 and higher). 2.0.4_cu8.0 is built with CUDA 8.0 which supports Pascal architecture GPUs. The '_SP' designation indicates 'single precision' CPU builds. All builds are single precision on the GPU and can be run on 'consumer-grade' GPU hardware.
196
-
197
-**RELION and MPI : **
198
-RELION uses the 'mpirun' executable to manage MPI ranks. SBGrid includes two OpenMPI versions, 2.1.2 (default) and 1.8.4 (legacy).
199
-The OpenMPI mpirun executable must match the version of OpenMPI used to build RELION.
200
-For example, RELION versions 2.1_cu*.0 use OpenMPI version 2.1.2 and must use mpirun from 2.1.2.
201
-
202
-Older RELION versions require an override in $HOME/.sbgrid.conf to set the older OpenMPI version to 1.8.4. Add
203
-
204
-OPENMPI_X=1.8.4"
205
-
206
-to $HOME/.sbgrid.conf and open a new terminal to use the correct mpirun.
207
-You can also use the 'mpirun.relion' executable in place of mpirun to use the MPI that matches the currently configured version of RELION.
208
-
209
-Links:
210
- Website: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
211
- Manual: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
212
- Forumhelp: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=CCPEM
213
-```
214
-
215
-### Installing and removing
216
-
217
-Install and remove titles with the *sbgrid install <title>* and *sbgrid remove <title>* command. Each of these commands can take multiple titles with versions at one time.
218
-
219
-**install**
220
-
221
-```
222
-install software title(s)
223
-
224
-Options:
225
- -d, --all-default install all default versions of all available software titles
226
- -a, --all-versions install all versions of all available software titles
227
- -c, --collection <collection> install all software titles from collection
228
- title@all install all versions of a software title
229
- title@x.y.z install "x.y.z" version of a software title
230
- -p, --progress-bar show progress bar during installation
231
- -y, --yes continue without confirmation
232
- -h, --help output usage information
233
-```
234
-
235
-**Install examples :**
236
-
237
-Install a single default version of an application :
238
-
239
-```
240
-./sbgrid-cli install relion
241
-```
242
-
243
-Install a specific version of a relion :
244
-
245
-```
246
- ./sbgrid-cli install relion@3.0.8
247
-```
248
-
249
-Install all versions of relion :
250
-
251
-```
252
- ./sbgrid-cli install relion@all
253
-```
254
-
255
-Install the 'Electron Microscopy' collection of titles (see above *list* command to list *collections*):
256
-
257
-```
258
- $ ./sbgrid-cli install -c 'Electron Microscopy'
259
-```
260
-
261
-Install all default versions of all titles :
262
-
263
-```
264
- ./sbgrid-cli install --all-defaults
265
-```
266
-
267
-Install all versions of all titles ( The full collection):
268
-
269
-```
270
- ./sbgrid-cli install --all-versions
271
-```
272
-
273
-**remove**
274
-
275
-Same options as install flag above.
276
-
277
-```
278
-remove software title(s)
279
-
280
-Options:
281
- -d, --all-default remove all default versions of all installed software titles
282
- -n, --non-default remove all non-default versions of all installed software titles
283
- -a, --all-versions remove all versions of all installed software titles
284
- -c, --collection <collection> remove all software titles from collection
285
- title@all remove all installed versions of a software title
286
- title@x.y.z remove "x.y.z" version of a software title
287
- -y, --yes continue without confirmation
288
- -h, --help output usage information
289
-```
290
-
291
-### Updating titles
292
-
293
-Updates are performed when default titles change to a new version or bugs are fixed in existing verisons. To update, use the update flag.
294
-
295
-**update**
296
-
297
-```
298
-./sbgrid-cli update relion
299
-```
300
-
301
-### Remove obsolete titles
302
-
303
-Use the obsolete flag to list or remove obsolete versions or titles
304
-
305
-**obsolete**
306
-
307
-```
308
- $ ./sbgrid-cli obsolete -h
309
-Usage: obsolete [options]
310
-
311
-list obsolete software versions
312
-
313
-Options:
314
- -r, --remove remove the obsolete software versions
315
- -y, --yes continue without confirmation
316
- -h, --help output usage information
317
-
318
-```
319
-
320
-## Advanced modes
321
-
322
-The advanced modes perform multiple actions and are designed for automated use for a managed 'rolling release' installation.
323
-
324
-**clean**
325
-
326
-Removes all obsolete software versions and titles
327
-
328
-**admin**
329
-
330
-Run periodic installation, update and removal. Installs all new titles, updates where appropriate and cleans up (removes) obsolete versions
331
-
332
-```
333
-Usage: admin [options]
334
-
335
-periodic update and installation
336
-
337
-Options:
338
- -a, --all-versions install all versions of all available software titles
339
- -r, --reinstall reinstall all of installed software titles
340
- -h, --help output usage information
341
-```
342
-
343
-For example running
344
-
345
-```
346
-./sbgrid-cli admin
347
-```
348
-
349
-will install all default, update all installed titles and remove all obsolete versions while
350
-
351
-```
352
-./sbgrid-cli admin -a
353
-```
354
-
355
-will install all versions of all titles, add any new titles, update any pending updates, and remove obsolete versions.
356
-This
357
-
358
-
359
-**rebuild**
360
-
361
-*rebuild* rebuilds the installation environment configuration files.
362
-
363
-**crontab**
364
-
365
-Writes a basic script for crontab for *admin* functionality
366
-
367
-**save**
368
-
369
-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).
370
-
371
-
372
-## Troubleshooting and diagnostics
373
-
374
-**check-connection**
375
-connectivity checks
376
-
377
-**diag**
378
-troubleshooting and diagnostics
379
-
380
-**verify**
381
-list missing software versions and .rc files
382
-
383
-## Installing software for multiple platforms
384
-
385
-On linux, add the --darwin command to install / remove for macOS .
386
-Conversely, use the --linux command to install / remove for Linux while on macOS.
387
-
388
-```
389
- --linux specify linux as platform
390
- --darwin specify macOS as platform
391
-```
392
-The platform flag is implied for the platform used to install the software.
393
-
394
-
395
-### Software Version Management in the SBGrid environment
396
-If you have a single version of an application installed, explicit version selection in your environment is not needed.
397
-
398
-In the case of multiple installed versions, the *SBGrid Default* version will be the version available at the terminal when it is installed, unless configured otherwise in *~/.sbgrid.conf*. This is standard for the SBGrid software environment.
399
-
400
-In the case of multiple non-default versions installed, the *latest release* will be version available in your shell. If you would like to have more than one version of a title installed, and prefer to use an older release or the non-default version when a default version is installed, you must set this explicitly in your *~/.sbgrid.conf* file. This is the same as in the standard SBGrid environment.
401
-
402
-**Version priority in the shell**
403
- 1. *~/.sbgrid.conf*
404
- 2. Installed single version
405
- 3. Installed Default version
406
- 4. Latest installed release
407
-
408
-There is more info on how to do that here --> [SBGrid version overrides](versions)
409
-
410
-### Running SBGrid software
411
-
412
-To use the software at the terminal in bash, open a new terminal and run
413
-
414
- $ source /programs/sbgrid.shrc
415
-
416
-or in tcsh
417
-
418
- $ source /programs/sbgrid.cshrc
419
-
420
-### Known Issues
421
-
422
-* **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)
423
-
424
-For help or to report issues, please email *bugs@sbgrid.org.*
cli_v2.md
... ...
@@ -0,0 +1,423 @@
1
+## SBGrid command line installation client - v2.0.44
2
+
3
+## How do I get it?
4
+[LINUX : sbgrid-cli_2.0.44_linux.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.0.44_linux.tar.gz)
5
+
6
+[macOS : sbgrid-cli_2.0.44_macOS.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.0.44_macOS.tar.gz)
7
+
8
+## Supported OSes
9
+[Linux (CentOS/RHEL 7 or 8 recommended) or Apple OSX computers running MacOSX v10.12 - 10.15.](operatingsystems)
10
+
11
+
12
+MacOS 10.15 Catalina can be used, but a work-around is required to add the /programs path.
13
+See [here for more info :](catalina)
14
+
15
+### Pre-installation requirements
16
+**Admin access required on your computer.**
17
+ The SBGrid installation client will install the software tree to /opt/sbgrid and create a symlink from this directory to /programs.
18
+ While admin privileges are not required to run the application, you will likely need admin privileges to create /opt/sbgrid and /programs .
19
+
20
+```
21
+ $ ./sbgrid-cli
22
+Usage: sbgrid-cli [command] [options]
23
+
24
+Commands:
25
+ help [command] command-specific help
26
+
27
+ activate [options] <site user key> | <credential-key> activate a new installation
28
+ reactivate [options] <configFilePath> [packagesPath] reactivate installation using config or package list
29
+
30
+ install [options] [title] [otherTitles...] install package(s)
31
+ remove|uninstall [options] [title] [otherTitles...] remove package(s)
32
+ reinstall [options] [title] [otherTitles...] reinstall package(s)
33
+ update|upgrade [options] [title] [otherTitles...] update package(s) to the latest release/version
34
+
35
+ list [options] [title] list available software titles
36
+ installed list installed software titles
37
+ updates list available updates
38
+ pending list pending installations
39
+ obsolete list obsolete software titles
40
+ search <query> search availble titles
41
+ collections list available package collections
42
+ grids list available software trees
43
+ info [options] [title] print title information
44
+ shell start SBGrid Shell
45
+
46
+ clean [options] remove obsolete software versions and titles
47
+ admin [options] run periodic installation, update and clean up
48
+ rebuild rebuild installation environment
49
+ crontab [options] basic script for crontab
50
+ save [filename] save current configuration
51
+
52
+ check-connection connectivity checks
53
+ diag [options] troubleshooting and diagnostics
54
+ verify list missing software versions and .rc files
55
+
56
+ Options:
57
+ -V, --version version
58
+ --verbose verbose output
59
+ --quiet disable output
60
+ -h, --help usage information
61
+ --linux specify linux as platform
62
+ --darwin specify macOS as platform
63
+ --no-color disable output colors
64
+```
65
+
66
+## General Usage
67
+The SBGrid command line installation client takes subcommands and arguments to those commands to perform various tasks. These can be found in the usage info shown above.
68
+Each subcommand can also take a -h or --help argument to show usage info.
69
+
70
+### Activation
71
+To install the software, you must have valid credentials provided by SBGrid.
72
+
73
+Activate with the 'activate' subcommand
74
+
75
+**activate**
76
+
77
+```
78
+Usage: activate [options] [site] [user] [key]
79
+
80
+activate new installation using credentials provided
81
+(credentials are sent via email and can either be a single credential-key, or a site username key triplet)
82
+
83
+Options:
84
+ -k, --credential-key <credential-key> activate with activation key
85
+ -h, --help output usage information
86
+```
87
+
88
+Trouble activating? See Troubleshooting options further down this page.
89
+
90
+**reactivate**
91
+
92
+*reactivate* can restore from a saved config file. See below.
93
+
94
+```
95
+ $ ./sbgrid-cli reactivate -h
96
+Usage: reactivate [options] <configFilePath> [packagesPath]
97
+
98
+reactivate a new instance of an installation using a “saved” configuration file
99
+to repair an existing installation see “reinstall --all-versions”
100
+
101
+Options:
102
+ --skip-folder-checking skip checking if folder with programs already exists
103
+ --just-activation skip software titles installation
104
+ -h, --help output usage information
105
+```
106
+
107
+### Listing available titles, status
108
+
109
+The *sbgrid list* command will show all available titles. They are normally colored by their installation status.
110
+Available options :
111
+
112
+**list**
113
+
114
+```
115
+Usage: list [options] [title] [otherTitles...]
116
+
117
+list available software titles
118
+
119
+Options:
120
+ -a, --all-versions list all available software versions
121
+ -d, --default-versions list default software versions
122
+ -c, --collections list available collections
123
+ -o, --one-column list software in one column
124
+ -l, --long-format list software versions in long format
125
+ -h, --help output usage information
126
+```
127
+
128
+**updates**
129
+
130
+Shows available updated version and titles
131
+
132
+```
133
+./sbgrid-cli updates
134
+```
135
+
136
+**obsolete**
137
+
138
+Shows obsolete versions that will be removed.
139
+Obsolete versions are previously installed versions no longer included in the SBGrid installation.
140
+
141
+```
142
+./sbgrid-cli obsolete
143
+```
144
+
145
+### Getting Information about titles
146
+
147
+**info**
148
+
149
+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.
150
+
151
+```
152
+Usage: info [options] [title] [otherTitles...]
153
+
154
+print software title(s) metadata
155
+
156
+Options:
157
+ -v, --versions list available and default versions for <title> on current platform
158
+ -c, --collections list available collections with software count
159
+ -h, --help output usage information
160
+```
161
+
162
+For example, info for RELION :
163
+
164
+```
165
+ $ ./sbgrid-cli info relion
166
+Fetching requested info...
167
+------------------------------------------------------------------------------------
168
+Package information for relion (i386-mac):
169
+
170
+Package: RELION
171
+Title: relion
172
+Architecture: i386-mac
173
+
174
+Available version(s):
175
+ * 1.3 (installed) depends on: openmpi (1.8.4)
176
+ * 1.4 (installed) depends on: openmpi (1.8.4)
177
+ * 2.1 (installed) depends on: openmpi (2.1.2)
178
+ * 3.0.6 (installed) depends on: openmpi (2.1.3)
179
+ * 3.0.7 (installed) depends on: openmpi (2.1.3)
180
+ * 3.0.8 (installed, default)
181
+ * 3.1-beta (installed)
182
+
183
+Grid(s): SBGrid
184
+Collection(s): Electron Microscopy
185
+
186
+Description:
187
+(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
188
+
189
+Technical notes:
190
+**GPU-accelerated RELION : ** RELION versions > 2.0 are GPU-accelerated using Nvidia CUDA on Linux.
191
+For general information on running GPU accelerated applications from SBGrid, please see here : https://sbgrid.org/wiki/gpu</a>
192
+
193
+CUDA builds of RELION are designated by a '_cu<cuda_version>' suffix in the version of the application.
194
+For example, 2.0.4_cu7.5 is linked against CUDA v7.5 libraries and is not recommended for Pascal architecture Nvidia hardware (GTX 1080 and higher). 2.0.4_cu8.0 is built with CUDA 8.0 which supports Pascal architecture GPUs. The '_SP' designation indicates 'single precision' CPU builds. All builds are single precision on the GPU and can be run on 'consumer-grade' GPU hardware.
195
+
196
+**RELION and MPI : **
197
+RELION uses the 'mpirun' executable to manage MPI ranks. SBGrid includes two OpenMPI versions, 2.1.2 (default) and 1.8.4 (legacy).
198
+The OpenMPI mpirun executable must match the version of OpenMPI used to build RELION.
199
+For example, RELION versions 2.1_cu*.0 use OpenMPI version 2.1.2 and must use mpirun from 2.1.2.
200
+
201
+Older RELION versions require an override in $HOME/.sbgrid.conf to set the older OpenMPI version to 1.8.4. Add
202
+
203
+OPENMPI_X=1.8.4"
204
+
205
+to $HOME/.sbgrid.conf and open a new terminal to use the correct mpirun.
206
+You can also use the 'mpirun.relion' executable in place of mpirun to use the MPI that matches the currently configured version of RELION.
207
+
208
+Links:
209
+ Website: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
210
+ Manual: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
211
+ Forumhelp: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=CCPEM
212
+```
213
+
214
+### Installing and removing
215
+
216
+Install and remove titles with the *sbgrid install <title>* and *sbgrid remove <title>* command. Each of these commands can take multiple titles with versions at one time.
217
+
218
+**install**
219
+
220
+```
221
+install software title(s)
222
+
223
+Options:
224
+ -d, --all-default install all default versions of all available software titles
225
+ -a, --all-versions install all versions of all available software titles
226
+ -c, --collection <collection> install all software titles from collection
227
+ title@all install all versions of a software title
228
+ title@x.y.z install "x.y.z" version of a software title
229
+ -p, --progress-bar show progress bar during installation
230
+ -y, --yes continue without confirmation
231
+ -h, --help output usage information
232
+```
233
+
234
+**Install examples :**
235
+
236
+Install a single default version of an application :
237
+
238
+```
239
+./sbgrid-cli install relion
240
+```
241
+
242
+Install a specific version of a relion :
243
+
244
+```
245
+ ./sbgrid-cli install relion@3.0.8
246
+```
247
+
248
+Install all versions of relion :
249
+
250
+```
251
+ ./sbgrid-cli install relion@all
252
+```
253
+
254
+Install the 'Electron Microscopy' collection of titles (see above *list* command to list *collections*):
255
+
256
+```
257
+ $ ./sbgrid-cli install -c 'Electron Microscopy'
258
+```
259
+
260
+Install all default versions of all titles :
261
+
262
+```
263
+ ./sbgrid-cli install --all-defaults
264
+```
265
+
266
+Install all versions of all titles ( The full collection):
267
+
268
+```
269
+ ./sbgrid-cli install --all-versions
270
+```
271
+
272
+**remove**
273
+
274
+Same options as install flag above.
275
+
276
+```
277
+remove software title(s)
278
+
279
+Options:
280
+ -d, --all-default remove all default versions of all installed software titles
281
+ -n, --non-default remove all non-default versions of all installed software titles
282
+ -a, --all-versions remove all versions of all installed software titles
283
+ -c, --collection <collection> remove all software titles from collection
284
+ title@all remove all installed versions of a software title
285
+ title@x.y.z remove "x.y.z" version of a software title
286
+ -y, --yes continue without confirmation
287
+ -h, --help output usage information
288
+```
289
+
290
+### Updating titles
291
+
292
+Updates are performed when default titles change to a new version or bugs are fixed in existing verisons. To update, use the update flag.
293
+
294
+**update**
295
+
296
+```
297
+./sbgrid-cli update relion
298
+```
299
+
300
+### Remove obsolete titles
301
+
302
+Use the obsolete flag to list or remove obsolete versions or titles
303
+
304
+**obsolete**
305
+
306
+```
307
+ $ ./sbgrid-cli obsolete -h
308
+Usage: obsolete [options]
309
+
310
+list obsolete software versions
311
+
312
+Options:
313
+ -r, --remove remove the obsolete software versions
314
+ -y, --yes continue without confirmation
315
+ -h, --help output usage information
316
+
317
+```
318
+
319
+## Advanced modes
320
+
321
+The advanced modes perform multiple actions and are designed for automated use for a managed 'rolling release' installation.
322
+
323
+**clean**
324
+
325
+Removes all obsolete software versions and titles
326
+
327
+**admin**
328
+
329
+Run periodic installation, update and removal. Installs all new titles, updates where appropriate and cleans up (removes) obsolete versions
330
+
331
+```
332
+Usage: admin [options]
333
+
334
+periodic update and installation
335
+
336
+Options:
337
+ -a, --all-versions install all versions of all available software titles
338
+ -r, --reinstall reinstall all of installed software titles
339
+ -h, --help output usage information
340
+```
341
+
342
+For example running
343
+
344
+```
345
+./sbgrid-cli admin
346
+```
347
+
348
+will install all default, update all installed titles and remove all obsolete versions while
349
+
350
+```
351
+./sbgrid-cli admin -a
352
+```
353
+
354
+will install all versions of all titles, add any new titles, update any pending updates, and remove obsolete versions.
355
+This
356
+
357
+
358
+**rebuild**
359
+
360
+*rebuild* rebuilds the installation environment configuration files.
361
+
362
+**crontab**
363
+
364
+Writes a basic script for crontab for *admin* functionality
365
+
366
+**save**
367
+
368
+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).
369
+
370
+
371
+## Troubleshooting and diagnostics
372
+
373
+**check-connection**
374
+connectivity checks
375
+
376
+**diag**
377
+troubleshooting and diagnostics
378
+
379
+**verify**
380
+list missing software versions and .rc files
381
+
382
+## Installing software for multiple platforms
383
+
384
+On linux, add the --darwin command to install / remove for macOS .
385
+Conversely, use the --linux command to install / remove for Linux while on macOS.
386
+
387
+```
388
+ --linux specify linux as platform
389
+ --darwin specify macOS as platform
390
+```
391
+The platform flag is implied for the platform used to install the software.
392
+
393
+
394
+### Software Version Management in the SBGrid environment
395
+If you have a single version of an application installed, explicit version selection in your environment is not needed.
396
+
397
+In the case of multiple installed versions, the *SBGrid Default* version will be the version available at the terminal when it is installed, unless configured otherwise in *~/.sbgrid.conf*. This is standard for the SBGrid software environment.
398
+
399
+In the case of multiple non-default versions installed, the *latest release* will be version available in your shell. If you would like to have more than one version of a title installed, and prefer to use an older release or the non-default version when a default version is installed, you must set this explicitly in your *~/.sbgrid.conf* file. This is the same as in the standard SBGrid environment.
400
+
401
+**Version priority in the shell**
402
+ 1. *~/.sbgrid.conf*
403
+ 2. Installed single version
404
+ 3. Installed Default version
405
+ 4. Latest installed release
406
+
407
+There is more info on how to do that here --> [SBGrid version overrides](versions)
408
+
409
+### Running SBGrid software
410
+
411
+To use the software at the terminal in bash, open a new terminal and run
412
+
413
+ $ source /programs/sbgrid.shrc
414
+
415
+or in tcsh
416
+
417
+ $ source /programs/sbgrid.cshrc
418
+
419
+### Known Issues
420
+
421
+* **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)
422
+
423
+For help or to report issues, please email *bugs@sbgrid.org.*
client_CLI_install.md
... ...
@@ -44,7 +44,7 @@ Binary releases of the install client are recommended - there is minimal install
44 44
45 45
[Mac : 1.0.694, 2018-03-21](downloads/sbgrid-1.0.694-Darwin.tgz)
46 46
47
-[Linux : 1.0.694, 2018-03-21](downloads/sbgrid-1.0.694-Linux.tgz)
47
+[Linux : 1.0.695, 2020-05-31](downloads/sbgrid-1.0.695-Linux.tgz)
48 48
49 49
```
50 50
$ tar -zxf sbgrid-1.0.694-Darwin.tgz