Bio-Roary
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CHANGELOG.md view on Meta::CPAN
# Change Log
## [Unreleased](https://github.com/sanger-pathogens/Roary/tree/HEAD)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.12.0...HEAD)
**Implemented enhancements:**
- Feature Request: Clear error message for duplicated file names [\#363](https://github.com/sanger-pathogens/Roary/issues/363)
**Fixed bugs:**
- uninitialized value warning [\#297](https://github.com/sanger-pathogens/Roary/issues/297)
- Bio::Root::Exception thrown during core genome alignment, missing some sequence in core\_gene\_alignment.aln [\#224](https://github.com/sanger-pathogens/Roary/issues/224)
**Closed issues:**
- Interpretation accessory\_binary\_genes newick [\#429](https://github.com/sanger-pathogens/Roary/issues/429)
- No gene annotation in gene\_presence\_absence.csv output [\#428](https://github.com/sanger-pathogens/Roary/issues/428)
- Compilation aborted at pan\_genome\_post\_analysis [\#427](https://github.com/sanger-pathogens/Roary/issues/427)
- Could not obtain pan\_genome\_sequences [\#426](https://github.com/sanger-pathogens/Roary/issues/426)
- Pan genome for fungal genomes [\#425](https://github.com/sanger-pathogens/Roary/issues/425)
- multifasta for all proteins [\#424](https://github.com/sanger-pathogens/Roary/issues/424)
- roary\_plots.py KeyError: "X" not in index [\#423](https://github.com/sanger-pathogens/Roary/issues/423)
- Confirm that use of BLAST's `-max\_target\_seqs` is intentional [\#422](https://github.com/sanger-pathogens/Roary/issues/422)
- query\_pan\_genome 'Cant access file' error \(Non-Working-Directory inputs\) [\#421](https://github.com/sanger-pathogens/Roary/issues/421)
- How many .gff files does Roary need? [\#419](https://github.com/sanger-pathogens/Roary/issues/419)
- Installation through Bioconda not working [\#418](https://github.com/sanger-pathogens/Roary/issues/418)
- Is it possible to run roary without prokka output files? [\#417](https://github.com/sanger-pathogens/Roary/issues/417)
- Exiting early because number of clusters is too high [\#415](https://github.com/sanger-pathogens/Roary/issues/415)
- MSG: Got a sequence without letters. Could not guess alphabet? [\#414](https://github.com/sanger-pathogens/Roary/issues/414)
- Which is the advantage to pre-use prokka to perform analysis using genbank \(.gbk and gbff\) files? [\#412](https://github.com/sanger-pathogens/Roary/issues/412)
- issues with running and empty files [\#411](https://github.com/sanger-pathogens/Roary/issues/411)
- MSG: Got a sequence without letters. Could not guess alphabet [\#410](https://github.com/sanger-pathogens/Roary/issues/410)
- moose.pm issue [\#407](https://github.com/sanger-pathogens/Roary/issues/407)
- Tutorial data: extract\_proteome\_from\_gff [\#406](https://github.com/sanger-pathogens/Roary/issues/406)
- Tutorial data: extract\_proteome\_from\_gff [\#403](https://github.com/sanger-pathogens/Roary/issues/403)
- gene\_presence\_absence.csv incomplete [\#402](https://github.com/sanger-pathogens/Roary/issues/402)
- Roary including non-protein coding features? [\#398](https://github.com/sanger-pathogens/Roary/issues/398)
- Question: what programs can be used to visualize embl and dot files? [\#394](https://github.com/sanger-pathogens/Roary/issues/394)
- Roary Does not terminated successfully [\#388](https://github.com/sanger-pathogens/Roary/issues/388)
- python: can't open file 'roary\_plots.py': \[Errno 2\] No such file or directory [\#385](https://github.com/sanger-pathogens/Roary/issues/385)
- Roary does not finish analysis even though cluster job queue returns successful completion [\#383](https://github.com/sanger-pathogens/Roary/issues/383)
- Genes \(well\) annotated in prokka end up all in different groups?? [\#355](https://github.com/sanger-pathogens/Roary/issues/355)
- could not determine version of cd-hit [\#322](https://github.com/sanger-pathogens/Roary/issues/322)
- Use of uninitialized value in require at \(eval 792\) line 1. [\#308](https://github.com/sanger-pathogens/Roary/issues/308)
- Error: unexpected input in "\_" [\#299](https://github.com/sanger-pathogens/Roary/issues/299)
- inconsistent referencing of $TMPDIR ? [\#287](https://github.com/sanger-pathogens/Roary/issues/287)
**Merged pull requests:**
- Include tests in README [\#430](https://github.com/sanger-pathogens/Roary/pull/430) ([ssjunnebo](https://github.com/ssjunnebo))
- 621556 badges [\#420](https://github.com/sanger-pathogens/Roary/pull/420) ([ssjunnebo](https://github.com/ssjunnebo))
- Update roary\_plots from .ix to .loc [\#416](https://github.com/sanger-pathogens/Roary/pull/416) ([EvdH0](https://github.com/EvdH0))
- Use only CDS features from GFF [\#400](https://github.com/sanger-pathogens/Roary/pull/400) ([embatty](https://github.com/embatty))
- also mention Devel::OverloadInfo and Digest::MD5::File as required Perl dependencies [\#397](https://github.com/sanger-pathogens/Roary/pull/397) ([boegel](https://github.com/boegel))
- Avoid deprecation errors in roary\_plots [\#389](https://github.com/sanger-pathogens/Roary/pull/389) ([mgalardini](https://github.com/mgalardini))
## [v3.12.0](https://github.com/sanger-pathogens/Roary/tree/v3.12.0) (2018-01-23)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.4...v3.12.0)
**Merged pull requests:**
- Reduce min gene size [\#384](https://github.com/sanger-pathogens/Roary/pull/384) ([ssjunnebo](https://github.com/ssjunnebo))
## [v3.11.4](https://github.com/sanger-pathogens/Roary/tree/v3.11.4) (2018-01-16)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.3...v3.11.4)
**Closed issues:**
- Roary seemed to have stopped prematurely; any way to continue the run? [\#380](https://github.com/sanger-pathogens/Roary/issues/380)
- Getting prank version without the online check [\#377](https://github.com/sanger-pathogens/Roary/issues/377)
- Kraken version parsing error: [\#376](https://github.com/sanger-pathogens/Roary/issues/376)
- 3.11.1 failing 2/55 \(3/791\) tests [\#375](https://github.com/sanger-pathogens/Roary/issues/375)
- Fix for prank version check [\#361](https://github.com/sanger-pathogens/Roary/issues/361)
- mafft version check still failing - bug in regexp found [\#360](https://github.com/sanger-pathogens/Roary/issues/360)
- roary -a =\> Use of uninitialized value in concatenation \(.\) [\#270](https://github.com/sanger-pathogens/Roary/issues/270)
**Merged pull requests:**
- Fix dependancy checking option [\#382](https://github.com/sanger-pathogens/Roary/pull/382) ([andrewjpage](https://github.com/andrewjpage))
## [v3.11.3](https://github.com/sanger-pathogens/Roary/tree/v3.11.3) (2018-01-12)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.2...v3.11.3)
**Merged pull requests:**
- Version fix [\#379](https://github.com/sanger-pathogens/Roary/pull/379) ([andrewjpage](https://github.com/andrewjpage))
## [v3.11.2](https://github.com/sanger-pathogens/Roary/tree/v3.11.2) (2018-01-12)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.1...v3.11.2)
**Fixed bugs:**
CHANGELOG.md view on Meta::CPAN
**Merged pull requests:**
- Fix empty accessory binary [\#264](https://github.com/sanger-pathogens/Roary/pull/264) ([andrewjpage](https://github.com/andrewjpage))
- change to dist zilla starter bundle [\#261](https://github.com/sanger-pathogens/Roary/pull/261) ([nds](https://github.com/nds))
## [v3.6.5](https://github.com/sanger-pathogens/Roary/tree/v3.6.5) (2016-07-20)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.4...v3.6.5)
**Merged pull requests:**
- allow new format bedtools and dont look for FASTA in GFF [\#260](https://github.com/sanger-pathogens/Roary/pull/260) ([andrewjpage](https://github.com/andrewjpage))
- catch divide by zero error [\#258](https://github.com/sanger-pathogens/Roary/pull/258) ([andrewjpage](https://github.com/andrewjpage))
## [v3.6.4](https://github.com/sanger-pathogens/Roary/tree/v3.6.4) (2016-07-06)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.3...v3.6.4)
**Merged pull requests:**
- drop testing for perl 5.10, add 5.24. dzil no longer works below 5.14 [\#257](https://github.com/sanger-pathogens/Roary/pull/257) ([andrewjpage](https://github.com/andrewjpage))
## [v3.6.3](https://github.com/sanger-pathogens/Roary/tree/v3.6.3) (2016-07-01)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.2...v3.6.3)
**Merged pull requests:**
- Speed up alignments [\#256](https://github.com/sanger-pathogens/Roary/pull/256) ([andrewjpage](https://github.com/andrewjpage))
## [v3.6.2](https://github.com/sanger-pathogens/Roary/tree/v3.6.2) (2016-05-10)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.1...v3.6.2)
**Implemented enhancements:**
- Prefix utility commands with roary- ? [\#226](https://github.com/sanger-pathogens/Roary/issues/226)
**Merged pull requests:**
- fix bug Can't exec /bin/sh: Argument list too long [\#247](https://github.com/sanger-pathogens/Roary/pull/247) ([duytintruong](https://github.com/duytintruong))
- get rid of warning message [\#246](https://github.com/sanger-pathogens/Roary/pull/246) ([satta](https://github.com/satta))
## [v3.6.1](https://github.com/sanger-pathogens/Roary/tree/v3.6.1) (2016-04-18)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.0...v3.6.1)
**Fixed bugs:**
- roary\_plots.py generating flawed plots [\#221](https://github.com/sanger-pathogens/Roary/issues/221)
**Closed issues:**
- Core gene file missing error [\#241](https://github.com/sanger-pathogens/Roary/issues/241)
**Merged pull requests:**
- prefix commands with roary [\#244](https://github.com/sanger-pathogens/Roary/pull/244) ([andrewjpage](https://github.com/andrewjpage))
- More improvements to roary\_plots [\#240](https://github.com/sanger-pathogens/Roary/pull/240) ([mgalardini](https://github.com/mgalardini))
## [v3.6.0](https://github.com/sanger-pathogens/Roary/tree/v3.6.0) (2016-02-23)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.9...v3.6.0)
**Fixed bugs:**
- MSG: Got a sequence without letters. Could not guess alphabet [\#229](https://github.com/sanger-pathogens/Roary/issues/229)
**Closed issues:**
- Roary 3.5.8 works with -i 80 switch, but not with -i 90 or higher with large datasets? [\#234](https://github.com/sanger-pathogens/Roary/issues/234)
- How to use multiple switches in commandline? [\#232](https://github.com/sanger-pathogens/Roary/issues/232)
**Merged pull requests:**
- Improvements to roary\_plots [\#236](https://github.com/sanger-pathogens/Roary/pull/236) ([mgalardini](https://github.com/mgalardini))
- Rollback 3 5 8 [\#235](https://github.com/sanger-pathogens/Roary/pull/235) ([andrewjpage](https://github.com/andrewjpage))
## [v3.5.9](https://github.com/sanger-pathogens/Roary/tree/v3.5.9) (2016-02-17)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.8...v3.5.9)
**Implemented enhancements:**
- What clusters end up in gene accessory\_binary\_genes.fa ? [\#225](https://github.com/sanger-pathogens/Roary/issues/225)
**Closed issues:**
- roary.github.io just prints HELLO [\#233](https://github.com/sanger-pathogens/Roary/issues/233)
**Merged pull requests:**
- Fix minor typo [\#231](https://github.com/sanger-pathogens/Roary/pull/231) ([abremges](https://github.com/abremges))
## [v3.5.8](https://github.com/sanger-pathogens/Roary/tree/v3.5.8) (2016-01-20)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.7...v3.5.8)
**Implemented enhancements:**
- Getting Roary into Debian Med [\#219](https://github.com/sanger-pathogens/Roary/issues/219)
- Add embl output file mapping location of each core gene in the core genome alignment [\#192](https://github.com/sanger-pathogens/Roary/issues/192)
**Closed issues:**
- Error message: Cannot find the mcxdeblast executable, please ensure its in your PATH [\#217](https://github.com/sanger-pathogens/Roary/issues/217)
**Merged pull requests:**
- Provide full accessory for building binary tree [\#227](https://github.com/sanger-pathogens/Roary/pull/227) ([andrewjpage](https://github.com/andrewjpage))
- roary\_plots: new fields in roary output must be parsed away [\#222](https://github.com/sanger-pathogens/Roary/pull/222) ([mgalardini](https://github.com/mgalardini))
- Debian nitpicks [\#220](https://github.com/sanger-pathogens/Roary/pull/220) ([satta](https://github.com/satta))
- Core alignment header file [\#218](https://github.com/sanger-pathogens/Roary/pull/218) ([andrewjpage](https://github.com/andrewjpage))
## [v3.5.7](https://github.com/sanger-pathogens/Roary/tree/v3.5.7) (2015-12-17)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.6...v3.5.7)
**Closed issues:**
- Roary not checking tools needed to run [\#214](https://github.com/sanger-pathogens/Roary/issues/214)
**Merged pull requests:**
- Core gene count [\#213](https://github.com/sanger-pathogens/Roary/pull/213) ([andrewjpage](https://github.com/andrewjpage))
## [v3.5.6](https://github.com/sanger-pathogens/Roary/tree/v3.5.6) (2015-12-01)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.5...v3.5.6)
**Implemented enhancements:**
CHANGELOG.md view on Meta::CPAN
- Accessory binary tree [\#155](https://github.com/sanger-pathogens/Roary/pull/155) ([andrewjpage](https://github.com/andrewjpage))
## [v3.0.3](https://github.com/sanger-pathogens/Roary/tree/v3.0.3) (2015-06-15)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.2...v3.0.3)
**Fixed bugs:**
- Annotation missing in set\_difference\_unique\_set\_one/two\_statistics.csv files [\#137](https://github.com/sanger-pathogens/Roary/issues/137)
**Merged pull requests:**
- when creating core gene alignment, lookup sample names to genes in sp… [\#153](https://github.com/sanger-pathogens/Roary/pull/153) ([andrewjpage](https://github.com/andrewjpage))
- Only align core files [\#150](https://github.com/sanger-pathogens/Roary/pull/150) ([andrewjpage](https://github.com/andrewjpage))
## [v3.0.2](https://github.com/sanger-pathogens/Roary/tree/v3.0.2) (2015-06-12)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.1...v3.0.2)
**Implemented enhancements:**
- Print out the version number [\#119](https://github.com/sanger-pathogens/Roary/issues/119)
**Merged pull requests:**
- Mafft and exonerate dependancies [\#149](https://github.com/sanger-pathogens/Roary/pull/149) ([andrewjpage](https://github.com/andrewjpage))
- Add a version parameter and add in marcos plots code [\#148](https://github.com/sanger-pathogens/Roary/pull/148) ([andrewjpage](https://github.com/andrewjpage))
## [v3.0.1](https://github.com/sanger-pathogens/Roary/tree/v3.0.1) (2015-06-12)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.0...v3.0.1)
**Fixed bugs:**
- Use of -e switch gives multifasta file with N's only [\#132](https://github.com/sanger-pathogens/Roary/issues/132)
## [v3.0.0](https://github.com/sanger-pathogens/Roary/tree/v3.0.0) (2015-06-11)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.4...v3.0.0)
**Merged pull requests:**
- Use prank for core genome alignments [\#147](https://github.com/sanger-pathogens/Roary/pull/147) ([andrewjpage](https://github.com/andrewjpage))
- Accessory graph [\#146](https://github.com/sanger-pathogens/Roary/pull/146) ([andrewjpage](https://github.com/andrewjpage))
## [v2.3.4](https://github.com/sanger-pathogens/Roary/tree/v2.3.4) (2015-06-10)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.3...v2.3.4)
## [v2.3.3](https://github.com/sanger-pathogens/Roary/tree/v2.3.3) (2015-06-08)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.2...v2.3.3)
**Merged pull requests:**
- Simplify perl dependency installation [\#145](https://github.com/sanger-pathogens/Roary/pull/145) ([bewt85](https://github.com/bewt85))
- Pan genome reference [\#144](https://github.com/sanger-pathogens/Roary/pull/144) ([andrewjpage](https://github.com/andrewjpage))
- Fix input files with duplicate IDs [\#143](https://github.com/sanger-pathogens/Roary/pull/143) ([andrewjpage](https://github.com/andrewjpage))
- Test against different versions of GNU Parallel [\#142](https://github.com/sanger-pathogens/Roary/pull/142) ([bewt85](https://github.com/bewt85))
## [v2.3.2](https://github.com/sanger-pathogens/Roary/tree/v2.3.2) (2015-06-08)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.1...v2.3.2)
**Fixed bugs:**
- GFF files derived from Prokka genbank raise errors [\#130](https://github.com/sanger-pathogens/Roary/issues/130)
- MSG: Got a sequence without letters. Could not guess alphabet [\#127](https://github.com/sanger-pathogens/Roary/issues/127)
**Merged pull requests:**
- TravisCI only wants the major and minor version of perl [\#141](https://github.com/sanger-pathogens/Roary/pull/141) ([bewt85](https://github.com/bewt85))
- Add TravisCI support [\#140](https://github.com/sanger-pathogens/Roary/pull/140) ([bewt85](https://github.com/bewt85))
- Use locus tag when ID is missing from GFF [\#139](https://github.com/sanger-pathogens/Roary/pull/139) ([andrewjpage](https://github.com/andrewjpage))
## [v2.3.1](https://github.com/sanger-pathogens/Roary/tree/v2.3.1) (2015-06-02)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.0...v2.3.1)
**Merged pull requests:**
- Extract IDs from GFF file using Bio::Perl [\#138](https://github.com/sanger-pathogens/Roary/pull/138) ([andrewjpage](https://github.com/andrewjpage))
## [v2.3.0](https://github.com/sanger-pathogens/Roary/tree/v2.3.0) (2015-06-01)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.6...v2.3.0)
**Closed issues:**
- "cpan" command reports Bio::Roary as version '\(undef\)' [\#134](https://github.com/sanger-pathogens/Roary/issues/134)
## [v2.2.6](https://github.com/sanger-pathogens/Roary/tree/v2.2.6) (2015-06-01)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.4...v2.2.6)
**Closed issues:**
- No tagged release for 2.2.3 [\#133](https://github.com/sanger-pathogens/Roary/issues/133)
- Syntax \(?\) errors on perl 5.10.1 [\#128](https://github.com/sanger-pathogens/Roary/issues/128)
**Merged pull requests:**
- include version numbers for cpan [\#136](https://github.com/sanger-pathogens/Roary/pull/136) ([andrewjpage](https://github.com/andrewjpage))
- New version number for contributed fix for issue \#128 [\#135](https://github.com/sanger-pathogens/Roary/pull/135) ([andrewjpage](https://github.com/andrewjpage))
- gnu parallel switch for ubuntu [\#131](https://github.com/sanger-pathogens/Roary/pull/131) ([andrewjpage](https://github.com/andrewjpage))
- Backward compatible deferencing of hashes [\#129](https://github.com/sanger-pathogens/Roary/pull/129) ([mgalardini](https://github.com/mgalardini))
## [v2.2.4](https://github.com/sanger-pathogens/Roary/tree/v2.2.4) (2015-05-29)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.3...v2.2.4)
**Closed issues:**
- ERROR: cannot remove directory for split\_groups [\#115](https://github.com/sanger-pathogens/Roary/issues/115)
- cleanup outputfiles [\#114](https://github.com/sanger-pathogens/Roary/issues/114)
**Merged pull requests:**
- Cleanup files [\#126](https://github.com/sanger-pathogens/Roary/pull/126) ([andrewjpage](https://github.com/andrewjpage))
## [v2.2.3](https://github.com/sanger-pathogens/Roary/tree/v2.2.3) (2015-05-21)
[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.2...v2.2.3)
**Closed issues:**
- Change QC so that it doesnt shred reads [\#117](https://github.com/sanger-pathogens/Roary/issues/117)
- QC doesnt work outside sanger [\#112](https://github.com/sanger-pathogens/Roary/issues/112)
**Merged pull requests:**
- Update Kraken QC [\#125](https://github.com/sanger-pathogens/Roary/pull/125) ([andrewjpage](https://github.com/andrewjpage))
( run in 2.184 seconds using v1.01-cache-2.11-cpan-524268b4103 )