Package: fastgenomics-cli
FASTGenomics CLIThis package is a collection of scripts to manage your data onFASTGenomics.It can be installed viapipinstallfastgenomics-cliand contains the following toolsFASTGenomics UploadThis script is used to upload files via the command line.Usagefg-upload[-h][-v][-dDATASET][-uUSER][-pPASSWORD][-tTITLE][-m][--dataset_typeDATASET_TYPE][--urlURL]file[file...]positionalarguments:filethefile(s)tobeuploaded

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verbosemoreverboseoutput(default:False)-dDATASET,--datasetDATASETaddfiletoexistingdatasetwiththisid(default:None)-uUSER,--userUSERyourusername(oremailaddress)(default:None)-pPASSWORD,--passwordPASSWORDyourpassword(default:None)-tTITLE,--titleTITLEthetitleofthenewdataset(default:None)-m,--metadatauploadfilesasmetadatainsteadofexpressiondata(default:False)--dataset_typeDATASET_TYPEthedatasettype(default:None)--urlURLTheplatformurl(default:https://beta.fastgenomics.org/)FASTGenomics CLIThis script is a generic command line interface for FASTGenomics.Usagefg-cli-houtputusage:fg-cli[-h]{login,logout,configure-aws,version,lfs,dataset}...________________________|____/\/____|____/____|(_)||__/\|(___||||________________________|__//\ \\___\|||||_|/_\'_ \ / _ \| '_`_\||/__/__|||/____\____)|||||__||__/|||(_)|||||||(__\__\|_|/_/\_\_____/|_|\_____|\___|_||_|\___/|_||_||_|_|\___|___/

WelcometoFASTGenomicsCLI!
Version0.12.0-c1

Herearethebasecommands:

optionalarguments:-h,--helpshowthishelpmessageandexitFASTGenomicsCLI:{login,logout,configure-aws,version,lfs,dataset}ActionsforFASTGenomicsloginLogintotheplatform.logoutLogouttoremoveaccesstotheplatform.configure-awsConfigureAWSfortheplatformversionShowtheversionofFASTGenomicsCLI.lfsManageLargeFileStorage(lfs)datasetManagedatasetscommonloginfg-clilogin-houtputusage:fg-clilogin[-h][-v][-uUSER][-pPASSPHRASE][-m{pat,password,bearer}][--urlURL]Logintotheplatform.

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verboseActivateverboseoutput-uUSER,--userUSERtheplatformuser-pPASSPHRASE,--passphrasePASSPHRASEthepassphraseofplatformuser-m{pat,password,bearer},--login_method{pat,password,bearer}theloginmethod'pat'(personalaccesstoken),'password'or'bearer'.Default:pat--urlURLtheurloftheplattform.ForExample:https://beta.fastgenomics.orglogoutfg-clilogout-houtputusage:fg-clilogout[-h][-v]Logouttoremoveaccesstotheplatform.

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verboseActivateverboseoutputversionfg-cliversion-houtputusage:fg-cliversion[-h][-v]Showtheversionofthecliclient

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verboseActivateverboseoutputdatasetfg-clidataset-houtputusage:fg-clidataset[-h]{get-types,get-type-details,create,upload-file,set-metadata,delete}...

Group:fgdataset-Managedatasets.

positionalarguments:{get-types,get-type-details,create,upload-file,set-metadata,delete}get-typesgetavailabledatasettypestogetherwiththeirnameanddescriptionget-type-detailsshowsalleditablefieldsforadatasettypecreatecreateadatasetupload-fileuploadfilestodatasetset-metadatasetthemetadataforadatasetdeletedeleteadataset

optionalarguments:-h,--helpshowthishelpmessageandexitget dataset typesfg-clidatasetget-types-houtputusage:fg-clidatasetget-types[-h][-v]getavailabledatasettypestogetherwiththeirnameanddescription

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verboseActivateverboseoutputget dataset type detailsfg-clidatasetget-type-details-houtputusage:fg-clidatasetget-type-details[-h][-v][-m{brief,full}][id]showsalleditablefieldsforadatasettypepositionalarguments:idtheidofthedatasettypeoptionalarguments:-h,--helpshowthishelpmessageandexit-v,--verboseActivateverboseoutput-m{brief,full},--mode{brief,full}descriptionmode.Either"full"or"brief".Default"brief".create a datasetfg-clidatasetcreate-houtputusage:fg-clidatasetcreate[-h][-v][-TTITLE][--dataset_typeDATASET_TYPE]createadataset

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verboseActivateverboseoutput-TTITLE,--titleTITLEthetitleofthedataset--dataset_typeDATASET_TYPEthedatasettype.Forexample"cs-singlecell".Togetanoverviewofavailabletypesuse`fg-clidatasetget-types`upload file to datasetfg-clidatasetupload-file-houtputusage:fg-clidatasetupload-file[-h][-v][-idID][-t[{primarydata,metadata}]]files[files...]uploadfilestodataset

positionalarguments:filesfilenamesofthefilestobeuploaded

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verboseActivateverboseoutput-idIDtheidofthedataset-t[{primarydata,metadata}],--type[{primarydata,metadata}]thetypeofthefile'primaryData'or'metaData':Default:primaryDataset metadata of a datasetfg-clidatasetset-metadata-houtputusage:fg-clidatasetset-metadata[-h][-v][-idID]metadatasetthemetadataforadataset

positionalarguments:metadatathemetadatetoset.Use@<filename>toprovidethedatabyfileor'{ json }'.Dependingonyoursystemyoumighthavetoescapequotesaccordingly.

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verboseActivateverboseoutput-idIDtheidofthedatasetset metadata by json stringfg-clidatasetset-metadata-iddataset-7463ed6a051b8557c7a03b33214e504e-d'{ "title": "new title" }'set metadata by file 'meta.json' containing the jsonfg-clidatasetset-metadata-iddataset-7463ed6a051b8557c7a03b33214e504e-d"@meta.json"delete datasetfg-clidatasetdelete-houtputusage:fg-clidatasetdelete[-h][-v]id

deleteadataset

positionalarguments:idtheidofthedataset

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verboseActivateverboseoutputlarge file storage (lfs)fg-clilfs-houtputusage:fg-clilfs[-h][-v]{create,get-url}...

Group:fglfs-ManageplatformLargeFileStorage(lfs)positionalarguments:{create,get-url}createCreateanduploadalargefilestorageget-urlGetadownloadurl

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verboseActivateverboseoutputcreate lfsfg-clilfscreate-houtputCreate and upload a large file storage

positional arguments:
  files_or_directory    file names or directory to be compressed

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         Activate verbose output
  -z [ZIP_FILENAME], --zip-filename [ZIP_FILENAME]
                        name of the zip file
  -P [ZIP_PASSWORD], --zip-password [ZIP_PASSWORD]
                        password for the zip file. if omitted a password will be generated.
  -r RECIPIENT_EMAIL, --recipient-email RECIPIENT_EMAIL
                        the email address used in the platform of the recipient
  -T [TITLE], --title [TITLE]
                        the title of the dataset containing the uploaded data
  --provider [{azure,aws}]
                        the provider to be used 'azure' or 'aws'. Default: azure)
  --skip-compression    Skip the compressionget url of lfsfg-clilfsget-url-houtputusage:fg-clilfsget-url[-h][-v]idaccess_token

Getadownloadurl

positionalarguments:idtheidofthestorageaccess_tokentheaccesstoken

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verboseActivateverboseoutputconfigure AWSfg-cliconfigure-aws-houtputusage:fg-cliconfigure-aws[-h][-v]ConfigureAWSfortheplatform

optionalarguments:-h,--helpshowthishelpmessageandexit-v,--verboseActivateverboseoutput