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ucsf-wynton / wynton-website-hpc

The Official Wynton HPC User Website
https://wynton.ucsf.edu/hpc/
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SBGrid: Add examples how to list available tools and how to use `sbwhich` #137

Open HenrikBengtsson opened 1 year ago

HenrikBengtsson commented 1 year ago

There's sbgrid-cli installed for this, but it doesn't work:

[hb-test@dev1 ~]$ sbgrid-cli installed --verbose
WARNING: read-only mode
-------

Found an existing SBGrid installation under /wynton/home/opt/sbgrid/programs, but the current user has limited access.
Only a subset of CLI commands are available. Run `sbgrid-cli help` for more info

debug: DEBUG output is enabled. IM version: 2.9.8
debug: Initializing the logs directory
debug: Initializing the installation client (flavor=sbgrid)
debug: Client parameters: {"logsDir":"/wynton/home/bengtsson/hb-test/.sbgrid/logs","logLevel":"debug","flavor":"sbgrid","baseURL":"https://sbgrid.org","architectures":["x86_64-linux"],"link":"/programs","disableAPICaching":false,"allowReadOnly":true}
debug: SBGrid client initialized
g: Constructor: ConfigParserErrors: File contains no section headers.
file: /wynton/home/bengtsson/hb-test/.sbgrid_installer line: 0
NaN
    at Re.run (/snapshot/sbgrid-client_v2/cli/node_modules/@caporal/core/dist/index.js:1:27912)
    at processTicksAndRejections (internal/process/task_queues.js:97:5)
    at process.runNextTicks [as _tickCallback] (internal/process/task_queues.js:66:3)
    at Function.runMain (pkg/prelude/bootstrap.js:1848:13)
    at internal/main/run_main_module.js:17:47 {
  meta: {
    error: Error: Constructor: ConfigParserErrors: File contains no section headers.
    file: /wynton/home/bengtsson/hb-test/.sbgrid_installer line: 0
    NaN
        at ConfigParserErrors.missingSectionHeaderError (/snapshot/sbgrid-client_v2/core/dist/corelib/package_manager/config/parser-errors.js:56:16)
        at /snapshot/sbgrid-client_v2/core/dist/corelib/package_manager/config/config-parser.js:133:64
        at Array.forEach (<anonymous>)
        at ConfigParser.read (/snapshot/sbgrid-client_v2/core/dist/corelib/package_manager/config/config-parser.js:122:15)
        at UserConfig.getSyncServer (/snapshot/sbgrid-client_v2/core/dist/corelib/package_manager/config/index.js:73:16)
        at new SBGridClient (/snapshot/sbgrid-client_v2/core/dist/corelib/client.js:136:39)
        at Function.<anonymous> (/snapshot/sbgrid-client_v2/core/dist/corelib/client.js:167:34)
        at step (/snapshot/sbgrid-client_v2/core/dist/corelib/client.js:33:23)
        at Object.next (/snapshot/sbgrid-client_v2/core/dist/corelib/client.js:14:53)
        at fulfilled (/snapshot/sbgrid-client_v2/core/dist/corelib/client.js:5:58)
  }
}

error: Constructor: ConfigParserErrors: File contains no section headers.
       file: /wynton/home/bengtsson/hb-test/.sbgrid_installer line: 0
       NaN

/snapshot/sbgrid-client_v2/cli/dist/cli.js:112
                        throw error;
                        ^

g: Constructor: ConfigParserErrors: File contains no section headers.
file: /wynton/home/bengtsson/hb-test/.sbgrid_installer line: 0
NaN
    at Re.run (/snapshot/sbgrid-client_v2/cli/node_modules/@caporal/core/dist/index.js:1:27912)
    at processTicksAndRejections (internal/process/task_queues.js:97:5)
    at process.runNextTicks [as _tickCallback] (internal/process/task_queues.js:66:3)
    at Function.runMain (pkg/prelude/bootstrap.js:1848:13)
    at internal/main/run_main_module.js:17:47 {
  meta: {
    error: Error: Constructor: ConfigParserErrors: File contains no section headers.
    file: /wynton/home/bengtsson/hb-test/.sbgrid_installer line: 0
    NaN
        at ConfigParserErrors.missingSectionHeaderError (/snapshot/sbgrid-client_v2/core/dist/corelib/package_manager/config/parser-errors.js:56:16)
        at /snapshot/sbgrid-client_v2/core/dist/corelib/package_manager/config/config-parser.js:133:64
        at Array.forEach (<anonymous>)
        at ConfigParser.read (/snapshot/sbgrid-client_v2/core/dist/corelib/package_manager/config/config-parser.js:122:15)
        at UserConfig.getSyncServer (/snapshot/sbgrid-client_v2/core/dist/corelib/package_manager/config/index.js:73:16)
        at new SBGridClient (/snapshot/sbgrid-client_v2/core/dist/corelib/client.js:136:39)
        at Function.<anonymous> (/snapshot/sbgrid-client_v2/core/dist/corelib/client.js:167:34)
        at step (/snapshot/sbgrid-client_v2/core/dist/corelib/client.js:33:23)
        at Object.next (/snapshot/sbgrid-client_v2/core/dist/corelib/client.js:14:53)
        at fulfilled (/snapshot/sbgrid-client_v2/core/dist/corelib/client.js:5:58)
  }
}