All public releases are listed below.

Release Raw Disk (Xen) VMWare/VirtualBox Date
clovr-1.0 RC9 clovr-standard-2017-03-03-23-18-44.img.gz clovr-standard-2017-03-03-23-18-44_vmdk.tar.gz (.vmdk)

clovr-standard-2017-03-03-23-18-44_vdi.tar.gz (.vdi)

March 3, 2017
clovr-1.0 RC8 clovr-standard-2016-06-07-02-13-51.img.gz clovr-standard-2016-06-07-02-13-51_vmdk.tar.gz (.vmdk)

clovr-standard-2016-06-07-02-13-51_vdi.tar.gz (.vdi)

June 7, 2016
clovr-1.0 RC7 clovr-standard-2015-08-06-19-44-18.img.gz clovr-standard-2015-08-06-19-44-18_vmdk.tgz (.vmdk)

clovr-standard-2015-08-06-19-44-18_vdi.tgz (.vdi)

Aug 27, 2015
clovr-1.0 RC6 clovr-standard-2014-10-07-21-11-54.img.gz clovr-standard-2014-10-07-21-11-54_vmdk.tgz (.vmdk)

clovr-standard-2014-10-07-21-11-54_vdi.tgz (.vdi)

Oct 10, 2014
clovr-1.0 RC5 clovr-standard-2012-11-16-20-05-15.img.gz clovr-standard-2012-11-16-20-05-15_vmdk.tgz (.vmdk)

clovr-standard-2012-11-16-20-05-15_vdi.tgz (.vdi)

Nov 27, 2012
clovr-1.0 RC4 clovr-standard-2012-05-14-13-47-28.img.gz clovr-standard-2012-05-14-13-47-28_vmdk.tgz (.vmdk)

clovr-standard-2012-05-14-13-47-28_vdi.tgz (.vdi)

May 15,2012
clovr-1.0 RC3 clovr-standard-2011-10-19-03-00-27.img.gz clovr-standard-2011-10-19-03-00-27_vmdk.tar.gz (.vmdk)

clovr-standard-2011-10-19-03-00-27.vdi.gz (.vdi)

Oct 26, 2011
clovr-1.0 RC2 clovr-standard-2011-08-24-11-04-17.img.gz clovr-standard-2011-08-25-05-13-27_vmdk.tgz (.vmdk)

clovr-standard-2011-08-25-05-13-27_vdi.tgz (.vdi)

Aug 25, 2011
clovr-1.0 RC1 clovr-standard-2011-07-01-11-04-17.img.gz clovr-standard-2011-07-01-11-04-17.tgz

clovr-standard-2011-07-01-11-04-17.vdi.gz (VDI)

Jul 1, 2011
clovr-beta-0.6 clovr-standard-2011-03-16-09-00-25.img.gz clovr-standard-2011-03-16-09-00-25.tgz Mar 16, 2011
clovr-beta-0.5 clovr-standard-2010-12-14-22-00-24.img.gz clovr-standard-2010-12-14-22-00-24.tgz Dec 14, 2010
clovr-beta-0.4.3 clovr-standard-2010-11-01-17-49-54-b3.img.gz clovr-standard-2010-11-01-17-49-54-b3.tgz Nov 8, 2010
clovr-beta-0.3 clovr-standard-2010-09-28-03-00-28.img.tgz clovr-standard-2010-09-28-03-00-28.tgz Sept 28, 2010
clovr-beta-0.2 clovr-standard-2010-09-02-00-40-38.img.tgz clovr-standard-2010-09-02-00-40-38.tgz Sept 2, 2010
clovr-beta-0.1 clovr.9-04.x86-64.beta-v1r29b1.img.gz clovr-vmware.beta-v1r29b1.tar.gz July 2010

Release clovr-1.0-RC9 (2017-03-03-23-18-44)

  • CloVR Comparative Pipeline
    • “mugsy_callsnps” component will now output VCF files, one per genome. These will be available as tagged output
    • The Circleator output figure has been updated. It now has changed colors and added track labels.

Release clovr-1.0-RC8 (2016-06-07-02-13-51)

  • CloVR 16S pipeline
    • Added ability to use 250-PE MiSeq FASTQ reads in pipeline
      • NOTE:  The pipeline will do the demultiplexing, so if your MiSeq reads are already demultiplexed, you can still run the pipeline by converting from FASTQ to FASTA
      • In the future, the ability to pass in demultiplexed FASTQ reads will be a feature.
    • Updated QIIME to v1.8 in the pipeline
    • Changed from de-novo OTU clustering to open-reference OTU clustering
  • CloVR Microbe pipeline
    • Added SPAdes assembly as an option for Illumina FASTQ reads
      • This will replace Velvet as the FASTQ assembler
    • Updated Microbe dashboard wizard to reflect changes
      • Do not have to specify short/long reads, or single-end/paired-end, since those were options specific to Velvet.  SPAdes will automatically determine if tag is single-end or paired-end.
    • Can now transfer Chado SQL annotation file and BER results to a Manatee VM for future genome annotation viewing and manual curation.
  • CloVR Comparative
    • Fixed issue where Sybil instances were broken by installing older version of MongoDB Perl CPAN module.
  • Various minor bug fixes

Release clovr-1.0-RC7 (2015-08-06-19-44-18)

  • Added default manatee database name to annotation pipeline
  • Renamed pipelines on clovr dashboard
  • Added display name to pipelines
  • Stripping out whitespace from urls to prevent any download errors when tagging
  • Fixed bsml2fasta missing key
  • Fixed template configs for missing keys
  • Added help button to dashboard
  • Added chado components to clovr-microbe to create database for use with Manatee VM
  • Corrected path for greengenes in qiime config
  • Added compiled files to updated qiime
  • Added new version of qiime (v1.8)
  • Updated CloVR-16S pipeline as qiime is updated
  • Fixes to accomodate for qiime 1.8 install
  • Updated qiime_config with greengenes path
  • Deleted greengenes from qiime-1.8
  • Adding greengenes phantom tag download
  • Removed hard-coded feature limit in histogram
  • Altering CPAN module path for a obsolete URI location
  • Adding content-disposition flag to reliableDownloader to allow it to follow redirects when a URL tag is passed
  • Changing sybil tarball to be downloaded from dropbox to CloVR S3 account
  • Separated out phylomark python dependency
  • Updated python recipe to install bx-python correctly

Release clovr-1.0-RC6 (2014-10-07-21-11-54)

  • Fixed bug in Comparative pipelines taxonomic tree search box where autocomplete results would sometimes be incorrect
  • Fixed bug where accession IDs would sometimes be missing from Microbe output files
  • Fixed bug where postgres would not start correctly on VM startup under VMware
  • Added a Genbank validation component to the Comparative pipeline
  • Updated the Genbank tree in the Comparative pipeline
  • Added ability to use Genbank accession ID’s as input to Comparative pipeline.
  • Added several UI and functionality improvements/bug fixes to the Sybil interface
  • Added FTP support to CloVR for uploading files

Release clovr-1.0-RC5

  • CloVR Microbe updated to version 2.0; includes hmmer3, updated annotation databases, and support for reference-based scaffold sequences
  • New protocols for HMP-DACC Walkthoughs: clovr_align_bowtie (indices and no indices), clovr_human_contaminan_screening, clovr_metagenomics_assembly
  • Added drop down on the dashboard to list ‘other’ pipelines
  • Security improvement; cannot terminate or start clusters remotely unless authorization check passes
  • Added preliminary support for importing clusters to create ad-hoc networks
  • Further improved stability in some of the back-end code for clusters
  • Added drop down on the dashboard to list ‘other’ pipelines

Release clovr-1.0-RC4

  • Improved support and robustness on DIAG cloud
  • Delete, resume support in UI
  • Default use of large instance type for Illumina assembly in CloVR-Microbe
  • Various UI tweaks

Release clovr-1.0-RC3

  • Support for patches and updates to running image
  • Support for automatic retries for failed pipelines
  • Numerous bug and usability fixes
  • Deploy of live demo site at
  • Improved support and reliability on DIAG
  • Bundled support for launching instances on DIAG

Release clovr-1.0-RC2

  • Fixes for networking problems at boot
  • Updated CloVR-16S v. 1.1 protocol and documentation with SOP and Nat. Prec. reference
  • Improved VirtualBox support. New VDI runs all pipelines on an auto-expanding partition.
  • Preliminary support for cloud-only mode
  • Added ability to add/remove files from existing datasets.
  • Now supports adding remotely hosted data files to datasets via URLs.
  • Fixed bugs in dataset addition and pipeline configuration.
  • Pipeline Grid is now sortable on pipeline ID.
  • Links to Ergatis pipelines are provided on in the header of the pipeline panel

Release clovr-1.0-RC1

  • New and improved web interface with support for adding data, running and monitoring pipelines, and configuring cloud support
  • Improved support for the DIAG cloud
  • Expanded output and published SOPs for the protocols, CloVR-microbe, CloVR-16S, CloVR-metagenomics
  • Robustness and reliability improvements
  • Improved API for programmatic access to the VM
  • VDI and expanding virtual disk support for VirtualBox

Release clovr-beta 0.6

  • Support for the DIAG cloud
  • Jobs run locally can now leverage multiple processor cores
  • Pipeline refinement
  • Prototype web interface at http://<your.image.ip.address>/clovr/dashboard.html

Release clovr-beta 0.5

  • Improved reliability, error reporting, and numerous bug fixes
  • New graphical startup screen and admin console
  • Updates to clovrMicrobe to match latest IGS Annotation Engine pipeline
  • Assembly (454 and Illumina) and genome annotation components of clovrMicrobe can all be run as stand-alone pipelines
  • Additional output and visualizations for 16s and metagenomics pipelines
  • Improvements to auto-scaling of cloud instances for BLAST, microbe, and metagenomics pipelines
  • Initial support for GBrowse
  • Initial pipeline for comparative genomics that predicts orthologs and characterizes a bacterial pan-genome (clovrComparative)
  • Initial pipeline for short read mapping using Bowtie or CrossBow (clovrMapping)
  • Initial support and testing for the DIAG academic cloud running Nimbus
  • Added documentation for the appliance API and web services that support provisioning virtual clusters, data transfer to/from the cloud, and executing workflows
  • Initial support for CloVR as a platform to build custom VMs. The latest Qiime VM was built using CloVR.

Release clovr-beta 0.4

  • Automated scaling of cluster instances for 454 and Illumina assembly and annotation pipelines (clovrMicrobe), clovrMetagenomics, and BLAST (clovrSearch)
  • Updated pipelines, documentation, SOPs, walk-throughs, and a new screencast
  • Improved support for VirtualBox
  • Numerous bug fixes, improved test suite, automated build process

Release clovr-beta 0.3

  • Bug fixes and improved documentation

Release clovr-beta 0.2

  • New CloVR16S
  • Updates to CloVRMicrobe for 454
  • There were also numerous technical developments on the backend, including
  • Upgrade to Ubuntu 10.04 ( kernel)
  • Recipes for building the VM with multiple editions: skeleton, base, standard
  • Automated builds and testing in Hudson
  • Standardization of the command line interface to vp-*
  • Merge of CloVR pipeline components with Ergatis trunk
  • Initial support for VirtualBox using OVF file
  • New cloud authentication scheme. vp-add-credential