Mercurial > repos > dereeper > roary_plots
view Roary/CHANGELOG.md @ 2:3f98630a0c20 draft
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| author | dereeper |
|---|---|
| date | Fri, 12 Nov 2021 16:30:50 +0000 |
| parents | c47a5f61bc9f |
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# 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:** - ExtractProteomeFromGff.t failing tests 3.11.0 [\#373](https://github.com/sanger-pathogens/Roary/issues/373) **Merged pull requests:** - fix mafft and kraken version extraction [\#378](https://github.com/sanger-pathogens/Roary/pull/378) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.11.1](https://github.com/sanger-pathogens/Roary/tree/v3.11.1) (2018-01-10) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.0...v3.11.1) **Closed issues:** - Sorting in version 3.11.0: uppercase letters first, lowercase second \(non-alphabetical\) [\#371](https://github.com/sanger-pathogens/Roary/issues/371) - Genbank input [\#365](https://github.com/sanger-pathogens/Roary/issues/365) - not all annotated features are allocated to the clusters [\#359](https://github.com/sanger-pathogens/Roary/issues/359) **Merged pull requests:** - Bedtools getfasta format fix [\#374](https://github.com/sanger-pathogens/Roary/pull/374) ([andrewjpage](https://github.com/andrewjpage)) - Update roary\_plots.py [\#372](https://github.com/sanger-pathogens/Roary/pull/372) ([franz89](https://github.com/franz89)) - Issue \#363 add check for duplicate basenames [\#370](https://github.com/sanger-pathogens/Roary/pull/370) ([nickp60](https://github.com/nickp60)) - README.md: Update Guix install instructions. [\#362](https://github.com/sanger-pathogens/Roary/pull/362) ([wwood](https://github.com/wwood)) ## [v3.11.0](https://github.com/sanger-pathogens/Roary/tree/v3.11.0) (2017-10-10) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.2...v3.11.0) **Fixed bugs:** - Can't get version of kraken, kraken-report or mafft ? [\#312](https://github.com/sanger-pathogens/Roary/issues/312) **Closed issues:** - number\_of\_conserved\_genes.Rtab [\#354](https://github.com/sanger-pathogens/Roary/issues/354) - \[question\] Should it take this long? [\#352](https://github.com/sanger-pathogens/Roary/issues/352) **Merged pull requests:** - change missing gene in core to be dashes rather than Ns [\#358](https://github.com/sanger-pathogens/Roary/pull/358) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.10.2](https://github.com/sanger-pathogens/Roary/tree/v3.10.2) (2017-09-08) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.1...v3.10.2) **Closed issues:** - \[version 3.8.0\] Roary crashes at end on perl error message [\#323](https://github.com/sanger-pathogens/Roary/issues/323) - Cant open file: \_accessory\_clusters.clstr [\#320](https://github.com/sanger-pathogens/Roary/issues/320) **Merged pull requests:** - get kraken version [\#351](https://github.com/sanger-pathogens/Roary/pull/351) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.10.1](https://github.com/sanger-pathogens/Roary/tree/v3.10.1) (2017-09-07) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.0...v3.10.1) **Implemented enhancements:** - Auto-detect if input files are GFF or FASTA [\#348](https://github.com/sanger-pathogens/Roary/issues/348) - Can "Fixing input GFF files" be parallelized? [\#342](https://github.com/sanger-pathogens/Roary/issues/342) **Fixed bugs:** - The GNU General Public License, Version not specified [\#344](https://github.com/sanger-pathogens/Roary/issues/344) **Closed issues:** - MSG: The sequence does not appear to be FASTA format \(lacks a descriptor line '\>'\) [\#346](https://github.com/sanger-pathogens/Roary/issues/346) **Merged pull requests:** - Improve input file handling [\#350](https://github.com/sanger-pathogens/Roary/pull/350) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.10.0](https://github.com/sanger-pathogens/Roary/tree/v3.10.0) (2017-09-07) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.9.1...v3.10.0) **Closed issues:** - Use of uninitialized value \(Perl\) [\#345](https://github.com/sanger-pathogens/Roary/issues/345) - identical .gff file names from different genome, and then issue with mcl groups [\#341](https://github.com/sanger-pathogens/Roary/issues/341) - Cant open file: \_clustered.clstr [\#339](https://github.com/sanger-pathogens/Roary/issues/339) ## [v3.9.1](https://github.com/sanger-pathogens/Roary/tree/v3.9.1) (2017-08-22) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.9.0...v3.9.1) **Merged pull requests:** - Optionally allow paralogs in core gene alignment [\#343](https://github.com/sanger-pathogens/Roary/pull/343) ([andrewjpage](https://github.com/andrewjpage)) - Script to find frequency of unique genes in samples [\#340](https://github.com/sanger-pathogens/Roary/pull/340) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.9.0](https://github.com/sanger-pathogens/Roary/tree/v3.9.0) (2017-08-09) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.2...v3.9.0) **Closed issues:** - roary\_plots: pangenome matrix tree does not look like input.newick tree [\#333](https://github.com/sanger-pathogens/Roary/issues/333) - use Roary with RAST files [\#332](https://github.com/sanger-pathogens/Roary/issues/332) - Roary [\#329](https://github.com/sanger-pathogens/Roary/issues/329) - sampling number is 10 in number of genes in pan and core genome [\#319](https://github.com/sanger-pathogens/Roary/issues/319) **Merged pull requests:** - Grammar edits [\#327](https://github.com/sanger-pathogens/Roary/pull/327) ([cgreene](https://github.com/cgreene)) - allow for inflation factor for MCL to be changed [\#326](https://github.com/sanger-pathogens/Roary/pull/326) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.8.2](https://github.com/sanger-pathogens/Roary/tree/v3.8.2) (2017-05-21) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.1...v3.8.2) ## [v3.8.1](https://github.com/sanger-pathogens/Roary/tree/v3.8.1) (2017-05-21) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.0...v3.8.1) **Closed issues:** - BLAST Database error [\#321](https://github.com/sanger-pathogens/Roary/issues/321) - Results for same input differ always a bit \(summary\_statistics.txt\) [\#318](https://github.com/sanger-pathogens/Roary/issues/318) - Error: Couldnt open GFF file [\#314](https://github.com/sanger-pathogens/Roary/issues/314) - Help with query\_pan\_genome [\#313](https://github.com/sanger-pathogens/Roary/issues/313) **Merged pull requests:** - update email address [\#325](https://github.com/sanger-pathogens/Roary/pull/325) ([ssjunnebo](https://github.com/ssjunnebo)) - New option to roary\_plots.py [\#317](https://github.com/sanger-pathogens/Roary/pull/317) ([mgalardini](https://github.com/mgalardini)) ## [v3.8.0](https://github.com/sanger-pathogens/Roary/tree/v3.8.0) (2017-01-25) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.7.1...v3.8.0) **Closed issues:** - Old version in the master tarball? [\#300](https://github.com/sanger-pathogens/Roary/issues/300) - prank is not installed \(Linuxbrew\) [\#294](https://github.com/sanger-pathogens/Roary/issues/294) - roary\_plots.py problem [\#292](https://github.com/sanger-pathogens/Roary/issues/292) **Merged pull requests:** - Support latest version of blast [\#306](https://github.com/sanger-pathogens/Roary/pull/306) ([andrewjpage](https://github.com/andrewjpage)) - infgen [\#305](https://github.com/sanger-pathogens/Roary/pull/305) ([andrewjpage](https://github.com/andrewjpage)) - update from 108 to 118 [\#304](https://github.com/sanger-pathogens/Roary/pull/304) ([andrewjpage](https://github.com/andrewjpage)) - update usage text for iterative CD-hit [\#301](https://github.com/sanger-pathogens/Roary/pull/301) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.7.1](https://github.com/sanger-pathogens/Roary/tree/v3.7.1) (2016-11-01) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.7.0...v3.7.1) **Closed issues:** - core\_gene\_alignment.aln missing [\#284](https://github.com/sanger-pathogens/Roary/issues/284) - Is these results fine to use? [\#282](https://github.com/sanger-pathogens/Roary/issues/282) **Merged pull requests:** - fix spelling [\#280](https://github.com/sanger-pathogens/Roary/pull/280) ([satta](https://github.com/satta)) - dont add POD to end of R scripts [\#279](https://github.com/sanger-pathogens/Roary/pull/279) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.7.0](https://github.com/sanger-pathogens/Roary/tree/v3.7.0) (2016-09-23) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.9...v3.7.0) ## [v3.6.9](https://github.com/sanger-pathogens/Roary/tree/v3.6.9) (2016-09-22) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.8...v3.6.9) **Implemented enhancements:** - I have published a Roary homebrew formula [\#208](https://github.com/sanger-pathogens/Roary/issues/208) - Getting Roary into Homebrew [\#152](https://github.com/sanger-pathogens/Roary/issues/152) **Closed issues:** - roary\_plots.py missing [\#277](https://github.com/sanger-pathogens/Roary/issues/277) - Errors when downloaded sequences from NCBI [\#274](https://github.com/sanger-pathogens/Roary/issues/274) - Same dataset different results! [\#271](https://github.com/sanger-pathogens/Roary/issues/271) - \_clustered.clstr file does not exist, cannot be read [\#250](https://github.com/sanger-pathogens/Roary/issues/250) **Merged pull requests:** - Fixed easy-init warnings - 529655 [\#278](https://github.com/sanger-pathogens/Roary/pull/278) ([psweston](https://github.com/psweston)) - README.md: Add instructions for GNU Guix. [\#273](https://github.com/sanger-pathogens/Roary/pull/273) ([wwood](https://github.com/wwood)) ## [v3.6.8](https://github.com/sanger-pathogens/Roary/tree/v3.6.8) (2016-08-02) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.7...v3.6.8) **Merged pull requests:** - Allow gene names from gb [\#266](https://github.com/sanger-pathogens/Roary/pull/266) ([andrewjpage](https://github.com/andrewjpage)) - Missing genes [\#265](https://github.com/sanger-pathogens/Roary/pull/265) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.6.7](https://github.com/sanger-pathogens/Roary/tree/v3.6.7) (2016-07-26) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.6...v3.6.7) **Fixed bugs:** - Roary 3.6.5 giving different \(erroneous\) results compared to 3.5.7 and 3.6.1/3.6.3/3.6.4 [\#263](https://github.com/sanger-pathogens/Roary/issues/263) - roary R plots don't work on server --- lack of X11 [\#194](https://github.com/sanger-pathogens/Roary/issues/194) **Closed issues:** - empty accessory\_binary\_genes.fa file [\#262](https://github.com/sanger-pathogens/Roary/issues/262) - a guix package [\#259](https://github.com/sanger-pathogens/Roary/issues/259) - create\_pan\_genome\_plots.R - X11 font problem [\#230](https://github.com/sanger-pathogens/Roary/issues/230) - Roary not generating pan\_genome\_reference.fa [\#223](https://github.com/sanger-pathogens/Roary/issues/223) - Roary not using packaged executables [\#215](https://github.com/sanger-pathogens/Roary/issues/215) ## [v3.6.6](https://github.com/sanger-pathogens/Roary/tree/v3.6.6) (2016-07-25) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.5...v3.6.6) **Fixed bugs:** - GFF parsing doesn't match GFF3 specification [\#249](https://github.com/sanger-pathogens/Roary/issues/249) **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:** - Non-issue, FYI regarding my 'roary2svg.pl' script [\#195](https://github.com/sanger-pathogens/Roary/issues/195) **Merged pull requests:** - add roary2svg script [\#212](https://github.com/sanger-pathogens/Roary/pull/212) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.5.5](https://github.com/sanger-pathogens/Roary/tree/v3.5.5) (2015-11-26) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.4...v3.5.5) **Merged pull requests:** - CD-hit threads limit [\#211](https://github.com/sanger-pathogens/Roary/pull/211) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.5.4](https://github.com/sanger-pathogens/Roary/tree/v3.5.4) (2015-11-26) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.3...v3.5.4) **Fixed bugs:** - Use of uninitialized value in require at \(eval ..\) line 1. [\#204](https://github.com/sanger-pathogens/Roary/issues/204) - \[bug\] Newick files in 3.5.1 have branch lengths of 0.0 [\#202](https://github.com/sanger-pathogens/Roary/issues/202) **Merged pull requests:** - Accessory binary fasta contains all C's fix [\#210](https://github.com/sanger-pathogens/Roary/pull/210) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.5.3](https://github.com/sanger-pathogens/Roary/tree/v3.5.3) (2015-11-26) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.2...v3.5.3) **Implemented enhancements:** - Enhancement: roary -a to continue on if other parameters as well [\#207](https://github.com/sanger-pathogens/Roary/issues/207) - Make summary\_statistics a TAB/TSV file? [\#193](https://github.com/sanger-pathogens/Roary/issues/193) **Fixed bugs:** - roary --version should return 0 not 255 exit code [\#206](https://github.com/sanger-pathogens/Roary/issues/206) - Is the roary -a check complete? [\#205](https://github.com/sanger-pathogens/Roary/issues/205) ## [v3.5.2](https://github.com/sanger-pathogens/Roary/tree/v3.5.2) (2015-11-25) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.1...v3.5.2) **Fixed bugs:** - Use of uninitialized value in File::Slurper and Encode.pm [\#196](https://github.com/sanger-pathogens/Roary/issues/196) **Merged pull requests:** - Improved dependancy checking [\#209](https://github.com/sanger-pathogens/Roary/pull/209) ([andrewjpage](https://github.com/andrewjpage)) - Lsf update gene alignments [\#201](https://github.com/sanger-pathogens/Roary/pull/201) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.5.1](https://github.com/sanger-pathogens/Roary/tree/v3.5.1) (2015-11-12) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.0...v3.5.1) **Fixed bugs:** - Accessory genes newick file contains full path of infividual files [\#200](https://github.com/sanger-pathogens/Roary/issues/200) - add optional dependancy from File::Slurper to stop warnings being printed [\#199](https://github.com/sanger-pathogens/Roary/pull/199) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.5.0](https://github.com/sanger-pathogens/Roary/tree/v3.5.0) (2015-11-12) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.3...v3.5.0) **Merged pull requests:** - remove path from accessory tree [\#198](https://github.com/sanger-pathogens/Roary/pull/198) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.4.3](https://github.com/sanger-pathogens/Roary/tree/v3.4.3) (2015-11-11) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.2...v3.4.3) **Merged pull requests:** - consensus group name for pan reference [\#190](https://github.com/sanger-pathogens/Roary/pull/190) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.4.2](https://github.com/sanger-pathogens/Roary/tree/v3.4.2) (2015-10-12) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.1...v3.4.2) **Merged pull requests:** - Gene presence and absence rtab [\#189](https://github.com/sanger-pathogens/Roary/pull/189) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.4.1](https://github.com/sanger-pathogens/Roary/tree/v3.4.1) (2015-10-08) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.0...v3.4.1) **Implemented enhancements:** - Need protein lengths in the final spreadsheet [\#116](https://github.com/sanger-pathogens/Roary/issues/116) **Fixed bugs:** - Bio-RetrieveAssemblies-1.0.1 fails to install [\#151](https://github.com/sanger-pathogens/Roary/issues/151) **Merged pull requests:** - \* Proposed fix for CPANTS error. [\#187](https://github.com/sanger-pathogens/Roary/pull/187) ([manwar](https://github.com/manwar)) ## [v3.4.0](https://github.com/sanger-pathogens/Roary/tree/v3.4.0) (2015-10-07) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.4...v3.4.0) **Merged pull requests:** - Extra columns in spreadsheet with gene lengths [\#186](https://github.com/sanger-pathogens/Roary/pull/186) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.3.4](https://github.com/sanger-pathogens/Roary/tree/v3.3.4) (2015-10-07) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.3...v3.3.4) **Closed issues:** - EXCEPTION: Bio::Root::Exception could not read ...faa.intermediate.extracted.fa [\#175](https://github.com/sanger-pathogens/Roary/issues/175) **Merged pull requests:** - increase dependancy RAM [\#185](https://github.com/sanger-pathogens/Roary/pull/185) ([andrewjpage](https://github.com/andrewjpage)) - Use lsf for gene alignment [\#184](https://github.com/sanger-pathogens/Roary/pull/184) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.3.3](https://github.com/sanger-pathogens/Roary/tree/v3.3.3) (2015-09-29) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.2...v3.3.3) **Merged pull requests:** - dont align if sequences same length and nearly the same [\#183](https://github.com/sanger-pathogens/Roary/pull/183) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.3.2](https://github.com/sanger-pathogens/Roary/tree/v3.3.2) (2015-09-28) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.1...v3.3.2) **Implemented enhancements:** - Use of temporary folders and files [\#177](https://github.com/sanger-pathogens/Roary/issues/177) **Merged pull requests:** - Duplicate sequences in pan genome reference fasta [\#182](https://github.com/sanger-pathogens/Roary/pull/182) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.3.1](https://github.com/sanger-pathogens/Roary/tree/v3.3.1) (2015-09-25) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.0...v3.3.1) **Merged pull requests:** - Fix usage text [\#181](https://github.com/sanger-pathogens/Roary/pull/181) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.3.0](https://github.com/sanger-pathogens/Roary/tree/v3.3.0) (2015-09-24) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.9...v3.3.0) **Fixed bugs:** - Check at least 2 gff files have been passed in [\#171](https://github.com/sanger-pathogens/Roary/issues/171) - Pentuple memory for worst case sCenario [\#170](https://github.com/sanger-pathogens/Roary/issues/170) - 00\_requires\_external.t missing "mafft" ? [\#168](https://github.com/sanger-pathogens/Roary/issues/168) **Merged pull requests:** - Check dependancies [\#180](https://github.com/sanger-pathogens/Roary/pull/180) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.2.9](https://github.com/sanger-pathogens/Roary/tree/v3.2.9) (2015-09-23) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.8...v3.2.9) **Implemented enhancements:** - Add --outdir option to avoid blatting current directory [\#176](https://github.com/sanger-pathogens/Roary/issues/176) **Fixed bugs:** - CPAN install failure "unknown option mafft" [\#169](https://github.com/sanger-pathogens/Roary/issues/169) **Closed issues:** - Error "Cant open file: \_uninflated\_mcl\_groups" [\#179](https://github.com/sanger-pathogens/Roary/issues/179) **Merged pull requests:** - Add the option to specify an output directory [\#178](https://github.com/sanger-pathogens/Roary/pull/178) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.2.8](https://github.com/sanger-pathogens/Roary/tree/v3.2.8) (2015-09-23) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.7...v3.2.8) ## [v3.2.7](https://github.com/sanger-pathogens/Roary/tree/v3.2.7) (2015-09-02) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.6...v3.2.7) **Merged pull requests:** - count paralogs correctly when looking for differences in datasets [\#174](https://github.com/sanger-pathogens/Roary/pull/174) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.2.6](https://github.com/sanger-pathogens/Roary/tree/v3.2.6) (2015-09-02) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.5...v3.2.6) **Merged pull requests:** - revert core tree generation [\#173](https://github.com/sanger-pathogens/Roary/pull/173) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.2.5](https://github.com/sanger-pathogens/Roary/tree/v3.2.5) (2015-08-17) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.4...v3.2.5) **Merged pull requests:** - Verbose stats [\#172](https://github.com/sanger-pathogens/Roary/pull/172) ([andrewjpage](https://github.com/andrewjpage)) - dont set bioperl version [\#167](https://github.com/sanger-pathogens/Roary/pull/167) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.2.4](https://github.com/sanger-pathogens/Roary/tree/v3.2.4) (2015-07-23) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.3...v3.2.4) **Merged pull requests:** - update readme citation [\#165](https://github.com/sanger-pathogens/Roary/pull/165) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.2.3](https://github.com/sanger-pathogens/Roary/tree/v3.2.3) (2015-07-22) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.1...v3.2.3) **Merged pull requests:** - update citation message [\#164](https://github.com/sanger-pathogens/Roary/pull/164) ([andrewjpage](https://github.com/andrewjpage)) - Pass mafft through to alignment [\#163](https://github.com/sanger-pathogens/Roary/pull/163) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.2.1](https://github.com/sanger-pathogens/Roary/tree/v3.2.1) (2015-07-21) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.0...v3.2.1) ## [v3.2.0](https://github.com/sanger-pathogens/Roary/tree/v3.2.0) (2015-07-20) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.2...v3.2.0) **Merged pull requests:** - Use mafft [\#162](https://github.com/sanger-pathogens/Roary/pull/162) ([andrewjpage](https://github.com/andrewjpage)) - output summary file [\#161](https://github.com/sanger-pathogens/Roary/pull/161) ([andrewjpage](https://github.com/andrewjpage)) - Pass through dont delete flag [\#160](https://github.com/sanger-pathogens/Roary/pull/160) ([andrewjpage](https://github.com/andrewjpage)) - Assembly statistics [\#159](https://github.com/sanger-pathogens/Roary/pull/159) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.1.2](https://github.com/sanger-pathogens/Roary/tree/v3.1.2) (2015-07-13) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/3.1.2...v3.1.2) ## [3.1.2](https://github.com/sanger-pathogens/Roary/tree/3.1.2) (2015-07-13) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.1...3.1.2) **Fixed bugs:** - prank seg fault [\#157](https://github.com/sanger-pathogens/Roary/issues/157) **Merged pull requests:** - Core gene missing files [\#158](https://github.com/sanger-pathogens/Roary/pull/158) ([andrewjpage](https://github.com/andrewjpage)) ## [v3.1.1](https://github.com/sanger-pathogens/Roary/tree/v3.1.1) (2015-06-26) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.0...v3.1.1) **Closed issues:** - sadaf [\#154](https://github.com/sanger-pathogens/Roary/issues/154) ## [v3.1.0](https://github.com/sanger-pathogens/Roary/tree/v3.1.0) (2015-06-22) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.3...v3.1.0) **Merged pull requests:** - 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)) ## [v2.2.2](https://github.com/sanger-pathogens/Roary/tree/v2.2.2) (2015-05-21) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.0...v2.2.2) **Closed issues:** - Hard-coded Sanger paths in some scripts [\#124](https://github.com/sanger-pathogens/Roary/issues/124) - You're missing some Perl dependancies [\#123](https://github.com/sanger-pathogens/Roary/issues/123) - Add support for GFF files from NCBI [\#120](https://github.com/sanger-pathogens/Roary/issues/120) **Merged pull requests:** - Fix usage text [\#122](https://github.com/sanger-pathogens/Roary/pull/122) ([andrewjpage](https://github.com/andrewjpage)) ## [v2.2.0](https://github.com/sanger-pathogens/Roary/tree/v2.2.0) (2015-05-14) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.1.2...v2.2.0) **Closed issues:** - Verbose output with -v [\#113](https://github.com/sanger-pathogens/Roary/issues/113) **Merged pull requests:** - Accept genbank files [\#121](https://github.com/sanger-pathogens/Roary/pull/121) ([andrewjpage](https://github.com/andrewjpage)) ## [v2.1.2](https://github.com/sanger-pathogens/Roary/tree/v2.1.2) (2015-05-12) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.1.1...v2.1.2) **Merged pull requests:** - Verbose output [\#118](https://github.com/sanger-pathogens/Roary/pull/118) ([andrewjpage](https://github.com/andrewjpage)) ## [v2.1.1](https://github.com/sanger-pathogens/Roary/tree/v2.1.1) (2015-04-29) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.9...v2.1.1) **Merged pull requests:** - pass core definition into number of conserved genes plot [\#111](https://github.com/sanger-pathogens/Roary/pull/111) ([andrewjpage](https://github.com/andrewjpage)) - Vary core definition [\#110](https://github.com/sanger-pathogens/Roary/pull/110) ([andrewjpage](https://github.com/andrewjpage)) - Use block quotes in readme [\#109](https://github.com/sanger-pathogens/Roary/pull/109) ([bewt85](https://github.com/bewt85)) ## [v2.0.9](https://github.com/sanger-pathogens/Roary/tree/v2.0.9) (2015-04-20) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.8...v2.0.9) **Merged pull requests:** - Allow for multiple processors to be used [\#108](https://github.com/sanger-pathogens/Roary/pull/108) ([andrewjpage](https://github.com/andrewjpage)) ## [v2.0.8](https://github.com/sanger-pathogens/Roary/tree/v2.0.8) (2015-04-09) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.7...v2.0.8) **Merged pull requests:** - Speedup [\#107](https://github.com/sanger-pathogens/Roary/pull/107) ([andrewjpage](https://github.com/andrewjpage)) - new version 2.0.7 [\#106](https://github.com/sanger-pathogens/Roary/pull/106) ([andrewjpage](https://github.com/andrewjpage)) ## [v2.0.7](https://github.com/sanger-pathogens/Roary/tree/v2.0.7) (2015-03-28) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.5...v2.0.7) **Merged pull requests:** - old splits [\#105](https://github.com/sanger-pathogens/Roary/pull/105) ([andrewjpage](https://github.com/andrewjpage)) - Speedup split [\#104](https://github.com/sanger-pathogens/Roary/pull/104) ([andrewjpage](https://github.com/andrewjpage)) ## [v2.0.5](https://github.com/sanger-pathogens/Roary/tree/v2.0.5) (2015-03-26) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/2.0.4...v2.0.5) **Merged pull requests:** - Stop deep recursion [\#103](https://github.com/sanger-pathogens/Roary/pull/103) ([andrewjpage](https://github.com/andrewjpage)) - check programs installed [\#102](https://github.com/sanger-pathogens/Roary/pull/102) ([andrewjpage](https://github.com/andrewjpage)) ## [2.0.4](https://github.com/sanger-pathogens/Roary/tree/2.0.4) (2015-03-23) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/2.0.3...2.0.4) **Merged pull requests:** - File slurp tiny [\#101](https://github.com/sanger-pathogens/Roary/pull/101) ([andrewjpage](https://github.com/andrewjpage)) - version 2.0.3 [\#100](https://github.com/sanger-pathogens/Roary/pull/100) ([andrewjpage](https://github.com/andrewjpage)) ## [2.0.3](https://github.com/sanger-pathogens/Roary/tree/2.0.3) (2015-03-17) [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.0...2.0.3) **Merged pull requests:** - Remove LSF support [\#99](https://github.com/sanger-pathogens/Roary/pull/99) ([andrewjpage](https://github.com/andrewjpage)) - Dont set LSF as the default runner [\#98](https://github.com/sanger-pathogens/Roary/pull/98) ([andrewjpage](https://github.com/andrewjpage)) - Rename directories to Roary [\#97](https://github.com/sanger-pathogens/Roary/pull/97) ([andrewjpage](https://github.com/andrewjpage)) ## [v2.0.0](https://github.com/sanger-pathogens/Roary/tree/v2.0.0) (2015-03-16) **Merged pull requests:** - Ship binaries [\#96](https://github.com/sanger-pathogens/Roary/pull/96) ([andrewjpage](https://github.com/andrewjpage)) - Pad merged multifastas when data is missing [\#95](https://github.com/sanger-pathogens/Roary/pull/95) ([carlacummins](https://github.com/carlacummins)) - Subsample reads [\#94](https://github.com/sanger-pathogens/Roary/pull/94) ([andrewjpage](https://github.com/andrewjpage)) - Merge Carlas CGN [\#93](https://github.com/sanger-pathogens/Roary/pull/93) ([andrewjpage](https://github.com/andrewjpage)) - rename spreadsheet [\#92](https://github.com/sanger-pathogens/Roary/pull/92) ([andrewjpage](https://github.com/andrewjpage)) - Refactor out fasta grep [\#91](https://github.com/sanger-pathogens/Roary/pull/91) ([andrewjpage](https://github.com/andrewjpage)) - remove fasta\_grep [\#90](https://github.com/sanger-pathogens/Roary/pull/90) ([andrewjpage](https://github.com/andrewjpage)) - Add gnu parallel support [\#89](https://github.com/sanger-pathogens/Roary/pull/89) ([andrewjpage](https://github.com/andrewjpage)) - Updated create\_pan\_genome help text to include -qc option [\#88](https://github.com/sanger-pathogens/Roary/pull/88) ([carlacummins](https://github.com/carlacummins)) - QC report option added [\#87](https://github.com/sanger-pathogens/Roary/pull/87) ([carlacummins](https://github.com/carlacummins)) - increase blastp min memory to 3gb from 100 [\#86](https://github.com/sanger-pathogens/Roary/pull/86) ([andrewjpage](https://github.com/andrewjpage)) - Remove fastatranslate dependancy [\#85](https://github.com/sanger-pathogens/Roary/pull/85) ([andrewjpage](https://github.com/andrewjpage)) - Queue set to basement if number of samples \> 600 \(previously 800\) [\#84](https://github.com/sanger-pathogens/Roary/pull/84) ([carlacummins](https://github.com/carlacummins)) - Bug fix [\#83](https://github.com/sanger-pathogens/Roary/pull/83) ([carlacummins](https://github.com/carlacummins)) - Added verbose stats option [\#82](https://github.com/sanger-pathogens/Roary/pull/82) ([carlacummins](https://github.com/carlacummins)) - Group limit changed to 50,000 [\#81](https://github.com/sanger-pathogens/Roary/pull/81) ([carlacummins](https://github.com/carlacummins)) - Multifastas not created when group limit \(default 8000\) exceeded [\#80](https://github.com/sanger-pathogens/Roary/pull/80) ([carlacummins](https://github.com/carlacummins)) - allow for translation table to be passed in [\#79](https://github.com/sanger-pathogens/Roary/pull/79) ([andrewjpage](https://github.com/andrewjpage)) - increase memory [\#78](https://github.com/sanger-pathogens/Roary/pull/78) ([andrewjpage](https://github.com/andrewjpage)) - Allow user specify sorting when reordering spreadsheet against a tree [\#77](https://github.com/sanger-pathogens/Roary/pull/77) ([andrewjpage](https://github.com/andrewjpage)) - Bug fixing [\#76](https://github.com/sanger-pathogens/Roary/pull/76) ([carlacummins](https://github.com/carlacummins)) - Added AUTHORS file [\#75](https://github.com/sanger-pathogens/Roary/pull/75) ([aslett1](https://github.com/aslett1)) - if theres more than 1k samples use basement for default analysis [\#74](https://github.com/sanger-pathogens/Roary/pull/74) ([andrewjpage](https://github.com/andrewjpage)) - use long queue for more than 200 samples [\#73](https://github.com/sanger-pathogens/Roary/pull/73) ([andrewjpage](https://github.com/andrewjpage)) - core alignment gets run with lsf [\#72](https://github.com/sanger-pathogens/Roary/pull/72) ([andrewjpage](https://github.com/andrewjpage)) - Job runner ids lsf [\#71](https://github.com/sanger-pathogens/Roary/pull/71) ([andrewjpage](https://github.com/andrewjpage)) - Core alignment missing file [\#70](https://github.com/sanger-pathogens/Roary/pull/70) ([andrewjpage](https://github.com/andrewjpage)) - Core alignment missing file [\#69](https://github.com/sanger-pathogens/Roary/pull/69) ([andrewjpage](https://github.com/andrewjpage)) - update error reporting [\#68](https://github.com/sanger-pathogens/Roary/pull/68) ([andrewjpage](https://github.com/andrewjpage)) - Create core alignment from spreadsheet and multifasta files [\#67](https://github.com/sanger-pathogens/Roary/pull/67) ([andrewjpage](https://github.com/andrewjpage)) - make script executable [\#66](https://github.com/sanger-pathogens/Roary/pull/66) ([andrewjpage](https://github.com/andrewjpage)) - script to merge multifasta files together [\#65](https://github.com/sanger-pathogens/Roary/pull/65) ([andrewjpage](https://github.com/andrewjpage)) - rename output gene multfastas and pass all sequences through [\#64](https://github.com/sanger-pathogens/Roary/pull/64) ([andrewjpage](https://github.com/andrewjpage)) - Align genes at protein level and back translate to nucleotides [\#63](https://github.com/sanger-pathogens/Roary/pull/63) ([andrewjpage](https://github.com/andrewjpage)) - Depth first search for reordering spreadsheet [\#62](https://github.com/sanger-pathogens/Roary/pull/62) ([andrewjpage](https://github.com/andrewjpage)) - make the iterative cdhit script useful for standalone use [\#61](https://github.com/sanger-pathogens/Roary/pull/61) ([andrewjpage](https://github.com/andrewjpage)) - query\_pan\_genome\_update\_text [\#60](https://github.com/sanger-pathogens/Roary/pull/60) ([andrewjpage](https://github.com/andrewjpage)) - fix failing tests [\#59](https://github.com/sanger-pathogens/Roary/pull/59) ([andrewjpage](https://github.com/andrewjpage)) - Create plot for % blast identity [\#58](https://github.com/sanger-pathogens/Roary/pull/58) ([andrewjpage](https://github.com/andrewjpage)) - add a flag to keep intermediate files [\#57](https://github.com/sanger-pathogens/Roary/pull/57) ([andrewjpage](https://github.com/andrewjpage)) - set the known gene names to black and rest to colours [\#56](https://github.com/sanger-pathogens/Roary/pull/56) ([andrewjpage](https://github.com/andrewjpage)) - print fragment blocks [\#55](https://github.com/sanger-pathogens/Roary/pull/55) ([andrewjpage](https://github.com/andrewjpage)) - Fix ordering of accessory [\#54](https://github.com/sanger-pathogens/Roary/pull/54) ([andrewjpage](https://github.com/andrewjpage)) - fix r plots [\#53](https://github.com/sanger-pathogens/Roary/pull/53) ([andrewjpage](https://github.com/andrewjpage)) - Overlapping proteins [\#52](https://github.com/sanger-pathogens/Roary/pull/52) ([andrewjpage](https://github.com/andrewjpage)) - Gene order [\#51](https://github.com/sanger-pathogens/Roary/pull/51) ([andrewjpage](https://github.com/andrewjpage)) - pass job runner to iterative cdhit [\#50](https://github.com/sanger-pathogens/Roary/pull/50) ([andrewjpage](https://github.com/andrewjpage)) - iterative cdhit in a job [\#49](https://github.com/sanger-pathogens/Roary/pull/49) ([andrewjpage](https://github.com/andrewjpage)) - Fix tests [\#48](https://github.com/sanger-pathogens/Roary/pull/48) ([andrewjpage](https://github.com/andrewjpage)) - Prefilter optimisation [\#47](https://github.com/sanger-pathogens/Roary/pull/47) ([andrewjpage](https://github.com/andrewjpage)) - dont split groups [\#46](https://github.com/sanger-pathogens/Roary/pull/46) ([andrewjpage](https://github.com/andrewjpage)) - rename create plots R script [\#45](https://github.com/sanger-pathogens/Roary/pull/45) ([andrewjpage](https://github.com/andrewjpage)) - cdhit should output full description of sequence name [\#44](https://github.com/sanger-pathogens/Roary/pull/44) ([andrewjpage](https://github.com/andrewjpage)) - Gene count plot [\#43](https://github.com/sanger-pathogens/Roary/pull/43) ([andrewjpage](https://github.com/andrewjpage)) - align gene multifasta files using muscle [\#42](https://github.com/sanger-pathogens/Roary/pull/42) ([andrewjpage](https://github.com/andrewjpage)) - Reorder spreadsheet [\#41](https://github.com/sanger-pathogens/Roary/pull/41) ([andrewjpage](https://github.com/andrewjpage)) - Reorder spreadsheet [\#40](https://github.com/sanger-pathogens/Roary/pull/40) ([andrewjpage](https://github.com/andrewjpage)) - Speedup post analysis [\#39](https://github.com/sanger-pathogens/Roary/pull/39) ([andrewjpage](https://github.com/andrewjpage)) - Presence and absence of genes [\#38](https://github.com/sanger-pathogens/Roary/pull/38) ([andrewjpage](https://github.com/andrewjpage)) - split big groups based on annotation [\#37](https://github.com/sanger-pathogens/Roary/pull/37) ([andrewjpage](https://github.com/andrewjpage)) - make multifasta files easier to sort [\#36](https://github.com/sanger-pathogens/Roary/pull/36) ([andrewjpage](https://github.com/andrewjpage)) - dont wait in lfs scheduler [\#35](https://github.com/sanger-pathogens/Roary/pull/35) ([andrewjpage](https://github.com/andrewjpage)) - run post analysis as a job [\#34](https://github.com/sanger-pathogens/Roary/pull/34) ([andrewjpage](https://github.com/andrewjpage)) - annotate the names of the groups files [\#33](https://github.com/sanger-pathogens/Roary/pull/33) ([andrewjpage](https://github.com/andrewjpage)) - Output all sequences making up pan genome in multifasta files [\#32](https://github.com/sanger-pathogens/Roary/pull/32) ([andrewjpage](https://github.com/andrewjpage)) - Run external applications through lsf [\#31](https://github.com/sanger-pathogens/Roary/pull/31) ([andrewjpage](https://github.com/andrewjpage)) - remove done dependancy job [\#30](https://github.com/sanger-pathogens/Roary/pull/30) ([andrewjpage](https://github.com/andrewjpage)) - blocking job [\#29](https://github.com/sanger-pathogens/Roary/pull/29) ([andrewjpage](https://github.com/andrewjpage)) - Filter unknowns in LSF jobs [\#28](https://github.com/sanger-pathogens/Roary/pull/28) ([andrewjpage](https://github.com/andrewjpage)) - Pass job runner through to extract gffs [\#27](https://github.com/sanger-pathogens/Roary/pull/27) ([andrewjpage](https://github.com/andrewjpage)) - Change case of GFF commandline class [\#26](https://github.com/sanger-pathogens/Roary/pull/26) ([andrewjpage](https://github.com/andrewjpage)) - use LSF to do the inital parsing of input files [\#25](https://github.com/sanger-pathogens/Roary/pull/25) ([andrewjpage](https://github.com/andrewjpage)) - renamed LICENSE [\#24](https://github.com/sanger-pathogens/Roary/pull/24) ([CraigPorter](https://github.com/CraigPorter)) - GPL [\#23](https://github.com/sanger-pathogens/Roary/pull/23) ([andrewjpage](https://github.com/andrewjpage)) - lsf memory in mb [\#22](https://github.com/sanger-pathogens/Roary/pull/22) ([andrewjpage](https://github.com/andrewjpage)) - low complexity filtering [\#21](https://github.com/sanger-pathogens/Roary/pull/21) ([andrewjpage](https://github.com/andrewjpage)) - inflate clusters where the representative gene is not the first [\#20](https://github.com/sanger-pathogens/Roary/pull/20) ([andrewjpage](https://github.com/andrewjpage)) - report more sequences from blastp [\#19](https://github.com/sanger-pathogens/Roary/pull/19) ([andrewjpage](https://github.com/andrewjpage)) - update tests for different input processing [\#18](https://github.com/sanger-pathogens/Roary/pull/18) ([andrewjpage](https://github.com/andrewjpage)) - speedup extracting proteins from gff [\#17](https://github.com/sanger-pathogens/Roary/pull/17) ([andrewjpage](https://github.com/andrewjpage)) - sort spreadsheet by number of isolates [\#16](https://github.com/sanger-pathogens/Roary/pull/16) ([andrewjpage](https://github.com/andrewjpage)) - create spreadsheets of differences between sets [\#15](https://github.com/sanger-pathogens/Roary/pull/15) ([andrewjpage](https://github.com/andrewjpage)) - Output statistics on groups [\#14](https://github.com/sanger-pathogens/Roary/pull/14) ([andrewjpage](https://github.com/andrewjpage)) - Find the difference between isolates [\#13](https://github.com/sanger-pathogens/Roary/pull/13) ([andrewjpage](https://github.com/andrewjpage)) - check if group is null [\#12](https://github.com/sanger-pathogens/Roary/pull/12) ([andrewjpage](https://github.com/andrewjpage)) - catch undef [\#11](https://github.com/sanger-pathogens/Roary/pull/11) ([andrewjpage](https://github.com/andrewjpage)) - tests for create pan genome script [\#10](https://github.com/sanger-pathogens/Roary/pull/10) ([andrewjpage](https://github.com/andrewjpage)) - label fasta sequences with annotation ID [\#9](https://github.com/sanger-pathogens/Roary/pull/9) ([andrewjpage](https://github.com/andrewjpage)) - extract proteomes from gffs and transfer anntotation as part of script [\#8](https://github.com/sanger-pathogens/Roary/pull/8) ([andrewjpage](https://github.com/andrewjpage)) - transfer annotation [\#7](https://github.com/sanger-pathogens/Roary/pull/7) ([andrewjpage](https://github.com/andrewjpage)) - speedup searching fastas [\#6](https://github.com/sanger-pathogens/Roary/pull/6) ([andrewjpage](https://github.com/andrewjpage)) - typo in memory estimation [\#5](https://github.com/sanger-pathogens/Roary/pull/5) ([andrewjpage](https://github.com/andrewjpage)) - run mcl and inflate results [\#4](https://github.com/sanger-pathogens/Roary/pull/4) ([andrewjpage](https://github.com/andrewjpage)) - vary memory usage according to input file size [\#3](https://github.com/sanger-pathogens/Roary/pull/3) ([andrewjpage](https://github.com/andrewjpage)) - working on real data [\#2](https://github.com/sanger-pathogens/Roary/pull/2) ([andrewjpage](https://github.com/andrewjpage)) - Initial functionality [\#1](https://github.com/sanger-pathogens/Roary/pull/1) ([andrewjpage](https://github.com/andrewjpage))