Package: cirro
Cirro ClientA Python 3.9+ library for the Cirro platform.InstallationYou can install Cirro using pip:pip install cirroor you can install the main branch of the repo by running:pip install git+https://github.com/CirroBio/Cirro-client.gitAuthenticationUpon first use, the Cirro client will ask if you would like to save your login information and give you a link to authenticate through the web browser.If you need to change your credentials after this point, and you've opted to save your login, please see theclearing saved loginsection.Command Line UsageDownloading a dataset:Usage:cirrodownload[OPTIONS]Downloaddatasetfiles

Options:--projectTEXTNameorIDoftheproject--datasetTEXTIDofthedataset--data-directoryTEXTDirectorytostorethefiles-i,--interactiveGatherargumentsinteractively--helpShowthismessageandexit.Uploading a dataset:Usage:cirroupload[OPTIONS]Uploadandcreateadataset

Options:--nameTEXTNameofthedataset--descriptionTEXTDescriptionofthedataset(optional)--projectTEXTNameorIDoftheproject--processTEXTNameorIDoftheingestprocess--data-directoryTEXTDirectoryyouwishtoupload-i,--interactiveGatherargumentsinteractively--helpShowthismessageandexit.Listing datasets:Usage:cirrolist-datasets[OPTIONS]Listavailabledatasets

Options:--projectTEXTIDoftheproject-i,--interactiveGatherargumentsinteractively--helpShowthismessageandexit.Interactive CommandsWhen running a command, you can specify the--interactiveflag to gather the command arguments interactively.Example:$cirroupload--interactive
?Whatprojectisthisdatasetassociatedwith?Testproject
?Enterthefullpathofthedatadirectory/shared/biodata/test
?Pleaseconfirmthatyouwishtoupload20files(0.630GB)Yes
?Whattypeoffiles?IlluminaSequencingRun
?Whatisthenameofthisdataset?test?Enteradescriptionofthedataset(optional)Python UsageSee the following set of Jupyter notebooks that contain examples on the following topics:Jupyter NotebookTopicIntroductionInstalling and authenticatingUploading a datasetUploading dataDownloading a datasetDownloading dataInteracting with a datasetCalling data and reading into tablesAnalyzing a datasetRunning analysis pipelinesUsing referencesManaging reference dataAdvanced usageAdvanced operationsR UsageJupyter NotebookTopicDownloading a dataset in RReading data with RAdvanced UsageView the API documentation for this libraryhere.Supported environment variablesNameDescriptionDefaultCIRRO_HOMELocal configuration directory~/.cirroCIRRO_BASE_URLBase URL of the data portalcirro.bioConfigurationThecirro configurecommand creates a file inCIRRO_HOMEcalledconfig.ini.You can set thebase_urlproperty in the config file rather than using the environment variable.Thetransfer_max_retriesconfiguration property specifies the maximum number of times to attempt uploading a file to Cirro in the event of a transfer failure.
When uploading files to Cirro, network issues or temporary outages can occasionally cause a transfer to fail.
It will pause for an increasing amount of time for each retry attempt.Theenable_additional_checksumsproperty manages the utilization of SHA-256 hashing for enhanced data integrity.
This feature computes the SHA-256 hash of a file during the upload process, and subsequently cross-validates it with the server upon completion.
When retrieving files, it ensures that the hash received matches the server's stored hash.
The default hashing algorithm for files is MD5. In many cases, MD5 is sufficient to ensure data integrity upon upload.[General]base_url=cirro.biotransfer_max_retries=15enable_additional_checksums=trueClearing saved loginYou can clear your saved login information by removing the~/.cirro/token.datfile from your system or
by runningcirro configureand selectingNowhen it asks if you'd like to save your login information.