All public releases are listed below.
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: Â 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
- Added ability to use 250-PE MiSeq FASTQ reads in pipeline
- 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. Â 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.
- Added SPAdes assembly as an option for Illumina FASTQ reads
- 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
- 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
- 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
- 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 live.clovr.org
- Improved support and reliability on DIAG
- Bundled support for launching instances on DIAG
- 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 (2.6.32.21 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