23eda6d405463742e317325c108b9411c092e210
sbgrid-cli.md
... | ... | @@ -24,16 +24,17 @@ Set up an account by registering here : [SBGrid registration](https://sbgrid.org |
24 | 24 | |
25 | 25 | [macOS : sbgrid-cli_2.1.3_macos.tar.gz](https://sbgrid.org/wiki/downloads/sbgrid-cli_2.1.3_macos.tar.gz) |
26 | 26 | |
27 | -MAC USERS PLEASE NOTE |
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28 | -If encounter a pop-up warning about "unidentified developer", you likely need to strip apple's quartine extended attribute. This is easy to do. |
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29 | 27 | |
30 | -Cancel the dialog and then run this in your terminal: |
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28 | +**MAC USERS PLEASE NOTE** |
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29 | +If you encounter a pop-up warning about an "unidentified developer", you need to strip apple's quartine extended attribute from the `sbgrid-cli` executable. This is easy to do. |
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30 | + |
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31 | +First, cancel the dialog and then run this in your terminal: |
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31 | 32 | |
32 | 33 | ``` |
33 | 34 | xattr -d com.apple.quarantine sbgrid-cli |
34 | 35 | ``` |
35 | 36 | |
36 | -You should then be able to run the application normally. |
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37 | +You should then be able to run the application normally without warnings. |
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37 | 38 | |
38 | 39 | ------------ |
39 | 40 | ## General Usage |
... | ... | @@ -54,7 +55,7 @@ To install the software, you must activate your installation with valid credenti |
54 | 55 | Activate with the `activate` subcommand |
55 | 56 | |
56 | 57 | ``` |
57 | - $ ./sbgrid-cli activate --help |
|
58 | + $ sbgrid-cli activate --help |
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58 | 59 | |
59 | 60 | SBGrid Installer 2.1.3 f593932a17 — |
60 | 61 | _______ _____ _ __ |
... | ... | @@ -109,7 +110,7 @@ Trouble activating? See Troubleshooting options further down this page. |
109 | 110 | **reactivate** subcommand can restore from a saved config file. This config includes all titles and versions from a saved installation. Useful for moving installations or reproducing installations. |
110 | 111 | |
111 | 112 | ``` |
112 | -sbgrid-cli reactivate <configPath> [OPTIONS...] |
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113 | + $ sbgrid-cli reactivate <configPath> [OPTIONS...] |
|
113 | 114 | ``` |
114 | 115 | |
115 | 116 | ### Listing available titles, status |
... | ... | @@ -175,7 +176,7 @@ Shows obsolete versions that will be removed. |
175 | 176 | Obsolete versions are previously installed versions no longer included in the SBGrid installation. |
176 | 177 | |
177 | 178 | ``` |
178 | -sbgrid-cli obsolete [OPTIONS...] |
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179 | + $ sbgrid-cli obsolete [OPTIONS...] |
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179 | 180 | ``` |
180 | 181 | |
181 | 182 | ### Getting Information about titles |
... | ... | @@ -185,13 +186,13 @@ sbgrid-cli obsolete [OPTIONS...] |
185 | 186 | The *info* subcommand shows information about each title, including a description and links to documentation can be show with the `sbgrid-cli info <title>` command. See example below. |
186 | 187 | |
187 | 188 | ``` |
188 | -sbgrid-cli info <title...> [OPTIONS...] |
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189 | + $ sbgrid-cli info <title...> [OPTIONS...] |
|
189 | 190 | ``` |
190 | 191 | |
191 | 192 | For example, info for *RELION* : |
192 | 193 | |
193 | 194 | ``` |
194 | -$ sbgrid-cli info relion |
|
195 | + $ sbgrid-cli info relion |
|
195 | 196 | ------------------------------------------------------------------------------------ |
196 | 197 | Package information for relion (x86_64-linux): |
197 | 198 | |
... | ... | @@ -301,7 +302,7 @@ Install all versions of *adxv* : |
301 | 302 | Install the 'Electron Microscopy' collection of titles (see above *list* command to list *collections*): |
302 | 303 | |
303 | 304 | ``` |
304 | - $ sbgrid-cli install -c 'Electron Microscopy' |
|
305 | + $ sbgrid-cli install -c 'Electron Microscopy' |
|
305 | 306 | ``` |
306 | 307 | |
307 | 308 | Install all default versions of all titles : |
... | ... | @@ -323,7 +324,7 @@ Note the `--reinstall` flag can be added to all commands to reinstall titles tha |
323 | 324 | Same options as install subcommand above. |
324 | 325 | |
325 | 326 | ``` |
326 | -sbgrid-cli remove [title...] [OPTIONS...] |
|
327 | +$ sbgrid-cli remove [title...] [OPTIONS...] |
|
327 | 328 | ``` |
328 | 329 | |
329 | 330 | ### Updating titles |
... | ... | @@ -343,7 +344,7 @@ Use the clean subcommand to list or remove obsolete versions or titles |
343 | 344 | **clean** |
344 | 345 | |
345 | 346 | ``` |
346 | -sbgrid-cli clean [OPTIONS...] |
|
347 | +$ sbgrid-cli clean [OPTIONS...] |
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347 | 348 | ``` |
348 | 349 | |
349 | 350 | ### Additional subcommands |
... | ... | @@ -355,7 +356,7 @@ sbgrid-cli clean [OPTIONS...] |
355 | 356 | Run periodic installation, update and removal. Installs all new titles, updates where appropriate and removes obsolete versions |
356 | 357 | |
357 | 358 | ``` |
358 | -sbgrid-cli admin |
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359 | +$ sbgrid-cli admin |
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359 | 360 | ``` |
360 | 361 | |
361 | 362 | For example running |
... | ... | @@ -422,7 +423,7 @@ These flags can be added to many of the subcommands to limit to Linux or macOS. |
422 | 423 | Useful for servers that share a software stack over NFS. |
423 | 424 | |
424 | 425 | ``` |
425 | -sbgrid-cli list --darwin |
|
426 | + $ sbgrid-cli list --darwin |
|
426 | 427 | ``` |
427 | 428 | This will list all software available for macOS. |
428 | 429 | The platform flag ( `--linux` or `--darwin`) is implied for the platform used to install the software, i.e. on linux, `--linux` is redundant. |