August 2014 CloudMan Release

August 8th 2014

CloudMan

We just released an update to Galaxy CloudMan. CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration.

This is mostly an incremental bug fix release with the following summary of changes:

  • On AWS, updated galaxyFS snapshot (snap-e6e1c04a), which includes the June 2, 2014 Galaxy release with the July 30th security fix. All the tools installed via the Tool Shed have been updated and a number of new tools added, most notably: Tophat2, Bowtie2, FastQC, several FASTQ manipulation tools, several QC tools.
  • For AWS, added support for VPC
  • For OpenStack clouds, added the ability to automatically recover worker instances on cluster reboot
  • Added support for creating a file system based on a downloadable archive
  • Do not run Galaxy with multiple processes by default. This is because Tool Shed installs do not work properly in the multi-process mode. This feature can be enabled by setting user data option configure_multiple_galaxy_processes to True when launching an instance.
  • Set SGE slots in each queue to be equal to the number of cores on the instance
  • Set instance IP in the Galaxy's FTP data upload tool message
  • Added support for Nginx v1.4 and allow it (with the PAM module) to used as the authentication mechanism when accessing Galaxy Reports app
  • Fixed cluster deletion when performed via the API
  • No longer automatically start Hadoop and HTCondor services
  • On manually-invoked instance reboots, do not increment the instance reboot count that otherwise eventually leads to instance termination
  • Limit the size of the log message buffer used in the UI to 1000 lines. Long-running instances had issues with this log growing large and that led to poor UI performance. The complete log is still available from the Admin page (or the command line).
  • Automatically delete the bucket/container for Test type (i.e, 'SGE only') clusters on cluster termination

For complete details on implemented changes, please see the source code commits.

Enjoy and please let us know what you think,

Enis & Dannon & The Galaxy Team