New BaseSpaceCLI Tools
We are pleased to announce the third release (version 0.8) of BaseSpaceCLI, which includes a major new tool and a number of minor features. To install the new release, run this script:
$ sudo bash -c "$(curl -L https://bintray.com/artifact/download/basespace/helper/install.sh)"
With this release of BaseSpaceCLI we are introducing a new high-performance copy tool called BaseSpace Copy or bscp, which provides the following features:
- Rich and flexible URI mechanism to specify source and target for copies
- Multi-threaded for performance and to cope with high-latency connections
- Excellent data integrity, all part data is hashed and verified. Ability to export md5sum compatible sum file for future data verification.
- Resumable downloading
Example Download (using default configuration):
Example Upload (using custom configuration):
For more information see the help documentation.
Should I use BaseMount or bscp?
BaseMount can also be used to copy files to and from BaseSpace. This table helps you choose which tool is most suitable for your application. A more detailed table is available in the help page.
|Browsing and interacting directly with files without having to download them locally||BaseMount|
|Interactive selective copying||BaseMount||The interactive nature of BaseMount makes it easier to select files to copy.|
|Programmatic selective copying||bscp||Bscp streams file metadata during copy and does not require the entire file tree to be loaded before copy starts.
Bscp requires no additional memory for complex filters.
|Scripted or programmatic copying||bscp||Using bscp in scripts avoids having to use a mount step.
Bscp has better error reporting as it has end-to-end control of data transfer.
Bscp will automatically close the AppSession when finished.
|Downloading runfolders with thousands of small files||bscp||BaseMount relies on Unix tools like cp and rsync, which only copy one file at a time. By copying more than one file in parallel, bscp performs better on these examples.|
Additional Improvements For This Release
To complement the other listing functions in BaseSpaceCLI we have introduced the
list runs command, which works just like the other entity listing tools.
For users working with multiple BaseSpace configurations, it can be useful to see details of the access tokens associated with each. The
whoami command provides this token reflection.
Again, the yaml, csv and json output options are also supported.
For Enterprise tier users, BaseSpace now provides support for examining a user’s event history and BaseSpaceCLI allows access to this stream of events. This can be accessed using the
bs history command. For more details, see the documentation.
As with previous releases, report bugs or other feedback on the Google Groups board.