Releases: TGAC/RAMPART
V0.12.2
V0.12.1
Bug fixes:
- Updated example configuration files to reflect new interface
- Fixed issue which prevented RAMPART working in unscheduled mode
- Fixed issue which prevented RAMPART working without mecq element in configuration file
- Fixed issue with multi stage AMP execution
v0.12.0
Implemented multi-sample handling. RAMPART can now execute the user defined receipe on multiple samples in parallel, and then perform a comparison of results between samples.
V0.11.3
Fixed a bug with the read input subsampler.
V0.11.2
Update to V0.11.2.
Fixed a bug with Kmer Genie (new conan release forces clients to specify files for stdout and stderr when process requires it). RAMPART now specifies logging infor from stderr goes to a file.
Updated ecoli example job config file so that thread counts are reduced. Also updated the organism element so it reflects the recent changes in the interface that V0.11.X expects.
If users are running in an unscheduled environment RAMPART forces all jobs to run linearly.
Release-0.11.0
Changes for V0.11.0
- Assembly selection step overhauled:
- User can provide a reference assembly for comparison via Quast, this enables use of NA50 and # missassemblies metrics. Interface changes in the element were required for this, RAMPART automatically calculates the # bases, GC% and # genes from reference automatically if provided, otherwise user can provide estimates of these metrics, or nothing at all.
- Metrics are now grouped into contiguity, problem, and conservation groups. Each group is assigned its own score, and the weighted average of these scores is now used to calculate the final assembly score.
- Documentation updated to include comparisons to other de novo assembly frameworks.
Release-0.10.3
- Made use of read kmer analysis optional.
- Made specification of sequence orientation mandatory only for paired reads.
- Enabled use of single end reads for SOAP scaffolder and gap closer.
Release-0.10.2
Changes in this release (since 0.9.0):
- Added kmer genie support
- Added Reapr support (for assembly enhancement - AMP)
- Using gene prediction for Quast for scoring assemblies
- Separated MASS assembly analysis from assembly selection stage
- Modified feature scaling algorithm for better assembly scoring
- Now have an addition category of MASS assembly (longest)
- Much improved input validation for the job configuration files
- Added a CITATION file to the root directory
- Updated job cleaner tool to include new directories
- Updated dependency downloader tool to include new dependencies
- Added pre-downloaded dependencies to this release
- Updated documentation
- Added description of "uniform" attribute for libraries
- Added a section on potential installation problems
- Added a section on potential runtime problems
- Added an example ecoli job configuration file for user testing
Release-0.9.0
Major upgrade to RAMPART. New features:
- Variable spreads - You can now optimise any assembly variable in the mass stage. For example, the min erosion parameter in Abyss, or the cov_cutoff in velvet.
- Checked and unchecked arguments - You can provide all tools in MECQ, MASS and AMP with "checked" and "unchecked" arguments. Checked arguments are parsed at startup to see if they are valid and recognized for the specific tool. Unchecked are just passed directly verbatim into the tools command line.
- AMP analyses - Rampart now can analyse assemblies produced at the AMP stage.
- Compressed output - RAMPART compresses the final output into a tarball for distribution
- Recognition and tracking of bubble files from those assemblers that produce them and when genome ploidy is 2. These can be used by platanus scaffolder.
- Improved configuration file validation
Current tool set:
Read Enhancement
Quake
Musket
Sickle
Assemblers
Abyss
ALLPATHS-LG
Platanus assemble
SOAP
Spades
Velvet
Assembly Enhancers
SOAP scaffolder
Platanus Scaffold
SSPACE Basic
SOAP gap close
Platanus gap close
Release-0.8.4
Finish Release-0.8.4