The NCBI Datasets project has developed command-line tools for downloading and converting biological data.
The datasets command-line tool is used to query and download biological sequence data across all domains of life from NCBI databases.
The dataformat command-line tool is used to convert metadata downloaded from NCBI Datasets from JSON lines format to other formats.
Both datasets and dataformat command-line tools are currently in alpha and will be updated frequently to add new features, fix bugs, and enhance usability. Command syntax is subject to frequent changes. Please check this page often for updates.
Download Aspera Client 2.7 for Mac from our website for free. Our built-in antivirus scanned this Mac download and rated it as 100% safe. This software for Mac OS X was originally developed by aspera. The program lies within Internet & Network Tools, more precisely Network tools. On command line, words in parameter names are separated by a dash, in configuration file, separator is an underscore.xxx-yyy on command line gives xxxyyy in configuration file. Note: before version 0.4.5, some keys could be ruby symbols, from 0.4.5 all keys are strings. To convert olver versions, remove the leading ':' in front of keys. ./aspera-connect-3.3.3.81344-linux-64.sh Testing From a web-browser. See the Aspera Documentation. From the Command Line. See also the Aspera ascp documentation. Test upload and download using a connection to the Aspera demo server, using password: demoaspera. Env ASPERASCPPASS=demoaspera /.aspera/connect/bin/ascp asperaweb@demo.asperasoft.
In response to the COVID-19 pandemic, we have recently added new functionality to allow retrieval of SARS-CoV-2 genome and protein datasets.
Latest release: 10.20.0 (2020-12-29)
HCC / packages / aspera-cli 3.9.1 0 IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. I had this same issue (and asked myself why anyone would use this over rsync), and then found the answer. It is extremely non-intuitive, but you must download the Aspera Connect browser plugin, and the CLI utility ascp is included in that package. If you still have issues, I have it in my Dropbox. Update: Aspera now maintains this shell script as a separate file.
Download the datasets tool
Download the datasets command-line tool.
Download the dataformat command-line tool.
To download datasets or dataformat from the command-line on Linux and Mac systems, you can alternatively use the curl command:
Linux
Download datasets using curl
Download dataformat using curl
Mac
Download datasets using curl
Download dataformat using curl
Running datasets and dataformat on Linux and Mac
Aspera Connect Download
To enable execution of datasets and dataformat on Linux and Mac systems, run the following command:
On Mac systems, you may need to explicitly allow running datasets and dataformat in Security & Privacy settings the first time you run them.
Getting help
Both datasets and dataformat command-line tools are currently in alpha and will be updated frequently to add new features, fix bugs, and enhance usability. Command syntax is subject to frequent changes. Please check this page often for updates.
Download Aspera Client 2.7 for Mac from our website for free. Our built-in antivirus scanned this Mac download and rated it as 100% safe. This software for Mac OS X was originally developed by aspera. The program lies within Internet & Network Tools, more precisely Network tools. On command line, words in parameter names are separated by a dash, in configuration file, separator is an underscore.xxx-yyy on command line gives xxxyyy in configuration file. Note: before version 0.4.5, some keys could be ruby symbols, from 0.4.5 all keys are strings. To convert olver versions, remove the leading ':' in front of keys. ./aspera-connect-3.3.3.81344-linux-64.sh Testing From a web-browser. See the Aspera Documentation. From the Command Line. See also the Aspera ascp documentation. Test upload and download using a connection to the Aspera demo server, using password: demoaspera. Env ASPERASCPPASS=demoaspera /.aspera/connect/bin/ascp asperaweb@demo.asperasoft.
In response to the COVID-19 pandemic, we have recently added new functionality to allow retrieval of SARS-CoV-2 genome and protein datasets.
Latest release: 10.20.0 (2020-12-29)
HCC / packages / aspera-cli 3.9.1 0 IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. I had this same issue (and asked myself why anyone would use this over rsync), and then found the answer. It is extremely non-intuitive, but you must download the Aspera Connect browser plugin, and the CLI utility ascp is included in that package. If you still have issues, I have it in my Dropbox. Update: Aspera now maintains this shell script as a separate file.
Download the datasets tool
Download the datasets command-line tool.
Download the dataformat command-line tool.
To download datasets or dataformat from the command-line on Linux and Mac systems, you can alternatively use the curl command:
Linux
Download datasets using curl
Download dataformat using curl
Mac
Download datasets using curl
Download dataformat using curl
Running datasets and dataformat on Linux and Mac
Aspera Connect Download
To enable execution of datasets and dataformat on Linux and Mac systems, run the following command:
On Mac systems, you may need to explicitly allow running datasets and dataformat in Security & Privacy settings the first time you run them.
Getting help
To get help in using the tools or any sub-commands specify --help after the command:
Aspera Connect Client Download
Check the version of datasets
Aspera Desktop Client Download
To get the version of datasets running on your machine, use the following command:
