You can upload your private data to CAVATICA using any of the following file transfer methods to suit your various requirements and achieve the best upload speed and reliability for the volume and structure of data that you are uploading.
Upload directly through CAVATICA's visual interface
The easiest and most intuitive way of uploading files to CAVATICA is to use the integrated upload functionality. This allows you to browse and select files from your local storage and upload them directly, without using additional tools or services. This upload method is most convenient and demonstrates best performance for small-scale uploads.
Upload using the Command-line (CLI) Uploader
If you have a larger volume of data on your local machine or cluster and want to upload it to CAVATICA (store it in CAVATICA storage), use the Command-line (CLI) Uploader. The CLI uploader is a fast and secure upload client that has been optimized to efficiently upload files to CAVATICA, taking advantage of parallelization where possible.
If the two recommended methods above are not convenient or suitable for your use case, you can also consider the following alternative upload option to bring data from your local storage to CAVATICA:
- Upload via the API. If you want to implement your own upload mechanism, you can use the CAVATICA API as a low-level method of uploading data to CAVATICA that treats a file as an ordered collection of smaller parts, manipulates multipart uploads, and offers more direct control over uploads.
If the data you want to bring to CAVATICA is located in a cloud storage service, rather than your local machine, here are the import methods you can use depending on the location of your data.
Import from a volume
If the data is already available on a cloud storage service (AWS S3 or Google Cloud Storage) and you want to use it on CAVATICA without transferring it to CAVATICA storage, use the Connect Cloud Storage feature.
If the data is available on an FTP or HTTP endpoint and you want to upload it to CAVATICA (store it in CAVATICA storage), use the HTTP(S)/FTP upload option.
This method is also used to upload data from a cloud storage service such as AWS S3 or Google Cloud Storage, using pre-signed URLs.
There are two file repositories on CAVATICA.
- Every project has its own Project Files. This repository is located within the project and contains the input and output files for workflows in that project. You can upload files directly to a project or copy them from other projects and repositories.
- Public Files, a repository of files maintained by our bioinformatics team, which contains the latest and most frequently used reference genomes and annotation files so you won't have to upload your own reference files every time you run a task. Many bioinformatics tools and workflows require reference and annotation files to work properly. If you cannot see the reference files you use for your analysis, please send us an email at [email protected], and we'll be sure to add them. Files stored in this repository can be copied to your Project Files for use in analyses.
Project Files can be viewed, edited, and copied by the project administrator and by project members with copy permissions.
Metadata is information about a file, such as specifics about the sequencing platform used to produce it. This information is linked to files and enables them to be searched and properly grouped for analyses. We recommend that you set the metadata fields for your input files before executing analyses on the Platform.
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