Recent Releases of circlator
circlator - Fixed dockerfile
Add install of headless default JRE to Dockerfile (fixes #140).
- Python
Published by Lfulcrum over 5 years ago
circlator - Docker image dependency check and tests fixed
Docker image fix - Locales were not properly set, breaks Circlator dependency checks (nucmer) when run in Singularity - Test files were not readable in Singularity
- Python
Published by trstickland about 6 years ago
circlator - AMOS and openpyxl dependency fixes
AMOS install to support minimus2 pipeline in docker image h/t Yuri Bendaña (ybendana) for working AMOS install -- see PR #151
openpyxl needs a downgrade to 2.6.4 to keep compatibility with circlator
- Python
Published by trstickland about 6 years ago
circlator - Fixed dockerfile
- docker build includes 2 extra debian packages
- docker build now builds from local repo (used to clone from github for every build, which was rather unconventional and made it harder to build with local changes)
- Python
Published by trstickland over 6 years ago
circlator - Improved version string handling for external dependancies
Plus some tests
- Python
Published by andrewjpage about 8 years ago
circlator - Version 1.5.1
Bug fixes (thanks @NicolaDM for reporting): - getting Canu version 1.5 - parsing canu output graph file
- Python
Published by martinghunt almost 9 years ago
circlator - Version 1.5.0
- Option to use Canu instead of SPAdes for reassemblies. Thanks to @NicolaDM for contributions.
- Python
Published by martinghunt almost 9 years ago
circlator - Version 1.4.1
Fixes a bug where --assemblenotonly_assembler caused it to crash (issue #80).
- Python
Published by martinghunt about 9 years ago
circlator - Version 1.4.0
Added options --fixstart_mincluster/--mincluster to change promer option -c|mincluster during fixstart stage.
- Python
Published by martinghunt over 9 years ago
circlator - Version 1.3.1
- bug fix with regex not matching, so sequences lost, when running get_dnaa
- Update the built-in dna FASTA file from uniprot (issue #73)
- Python
Published by martinghunt over 9 years ago
circlator - Version 1.3.0
- add --debug option to progcheck
- bug fix running spades (used to assume python2 was in path, but not any longer)
- drop dependency on bioassemblyrefinement python package
- add --verbose option to fixstart (see issue #57)
- bug fix handling whitespace in fasta headers with fixstart (see issue #64)
- bug fix incorrect break point coordinates in fixstart log
- Python
Published by martinghunt over 9 years ago
circlator - Version 1.2.1
No changes to algorithm or final fasta. Cosmetic changes related to logging: - bug fix reporting spades version (issue #56) - more verbose reporting of version numbers (particularly python package dependencies) - verbose added to bam2reads (issue #57) - When verbose, output final summary of contig numbers and circularizations (issue #55) - New option circlator all --unchanged_code, to let user choose return code when contigs unchanged (issue #55)
- Python
Published by martinghunt almost 10 years ago
circlator - Version 1.2.0
- options to not use the spades flags --careful (thanks again @gedankenstuecke) or not use --only-assembler.
- new command "test", which does a complete run of "circlator all" on a small built-in test data set.
- Python
Published by martinghunt almost 10 years ago
circlator - Version 1.1.5
- Supports samtools 1.2+ (thanks @gedankenstuecke)
- Require pysam version 0.8.1-0.8.3 (latest 0.9.0 does not install with Travis)
- Added unit tests for the mapping code
- Python
Published by martinghunt almost 10 years ago
circlator - Version 1.1.4
Bug fix where circularization sometimes failed (thanks to Jia-Xing Yue for reporting)
- Python
Published by martinghunt about 10 years ago
circlator - Version 1.1.3
Fixes bug when running the 'merge' task without --reads option (see issue #44).
- Python
Published by martinghunt about 10 years ago
circlator - Version 1.1.2
- Add support for SPAdes version 3.6.2.
- Remove support for SPAdes 3.6.1 (but older versions are OK) because it does not output graph information.
- Python
Published by martinghunt about 10 years ago
circlator - Version 1.1.1
Bug fixes to handle Spades version 3.6.1: - Circlator will work with it, but with less functionality - If spades version >3.6.0 is detected, lots of warning messages are output suggesting that 3.6.0 would be better instead.
Also bug fix using --nopairmerge (it was making the pipeline die).
- Python
Published by martinghunt over 10 years ago
circlator - Version 1.1.0
- change to how SPAdes is run: instead of using the first kmer that returns a successful assembly, all kmers are tried and the one with the largest N50 is used. The old behaviour can be run with the option --assemblespadesuse_first
- clearer logging. --verbose is now just for debugging. Useful information for the user about how/why merges were (not) made is now only in the log files.
- ACT files written to compare SPAdes reassemblies against current state of the assembly. Useful for troubleshooting
- SPAdes version must be 3.5.0 or 3.6.0. Currently Circlator will not work with 3.6.1.
- Python
Published by martinghunt over 10 years ago
circlator - Version 1.0.2
Removed a few false-positive dnaA genes from the default set used by fixstart.
- Python
Published by martinghunt over 10 years ago
circlator - Version 1.0.1
Add full paths to binaries when running progcheck: see issue #36.
- Python
Published by martinghunt over 10 years ago
circlator - Version 1.0.0
- get_dnaa can take a uniprot search term so any genes can be downloaded, instead of just dnaa.
- when running "circlator all...", writes a file 00.info.txt that has how circlator was run, the version of circlator, and versions of all the dependencies.
- Python
Published by martinghunt over 10 years ago
circlator - Version 0.16.1
- bug fix: stop trying to run spades with python3.4
- added travisCI
- Python
Published by martinghunt over 10 years ago
circlator - Version 0.16.0
- new task progcheck, which checks that Circlator can find the dependencies OK, and also that the versions are high enough
- new task get_dnaa. which generates a fasta file of dnaA genes, downloaded from uniprot.
- default set of dnaA genes now has 2,691 genes, instead of the old one that had <200 genes. Generated using new task get_dnaa
- default minimum % identity needed for a match to a dnaA gene dropped from 80% to 70%. This is now a parameter that the user can change
- Python
Published by martinghunt over 10 years ago
circlator - Version 0.15.1
Bug fix to stop crashing when --ignore not used when running circlator fixstart
- Python
Published by martinghunt over 10 years ago
circlator - Version 0.15.0
- New option to pull out contigs of interest (eg a mitochondrion from a eukaryote assembly)
- New option to discard unmapped reads instead of including them in the assembly
- New option to choose minimum read length
- Some sanity checking of input
- Python
Published by martinghunt over 10 years ago
circlator - Version 0.14.1
Rewrote clean stage to remove more contigs.
- Python
Published by martinghunt over 10 years ago
circlator - Version 0.14.0
Added option to let user choose the kmer(s) when running assemblies with SPAdes. Was previously hard-coded.
- Python
Published by martinghunt over 10 years ago
circlator - Version 0.13.2
Fixed bug where in rare cases contigs of size ~30-100kb were not recognised as circular.
- Python
Published by martinghunt over 10 years ago
circlator - Version 0.13.1
Bug fix to "minimus2" task. If minimus2 died on initial merge, then the whole script died. Fixed so that it carries on.
- Python
Published by martinghunt almost 11 years ago
circlator - Version 0.13.0
- added automated (slightly modified) implementation of PacBio's protocol using minimus2.
- tweaked nucmer options to improve results
- Python
Published by martinghunt almost 11 years ago
circlator - Version 0.12.1
Typos in usage fixed
- Python
Published by martinghunt almost 11 years ago
circlator - Version 0.12.0
Major algorithmic changes since version 0.2.0.
- Python
Published by martinghunt almost 11 years ago