Implemented enhancements:
- Feature Request: Clear error message for duplicated file names #363
Fixed bugs:
- uninitialized value warning #297
- Bio::Root::Exception thrown during core genome alignment, missing some sequence in core_gene_alignment.aln #224
Closed issues:
- Interpretation accessory_binary_genes newick #429
- No gene annotation in gene_presence_absence.csv output #428
- Compilation aborted at pan_genome_post_analysis #427
- Could not obtain pan_genome_sequences #426
- Pan genome for fungal genomes #425
- multifasta for all proteins #424
- roary_plots.py KeyError: "X" not in index #423
- Confirm that use of BLAST's
-max\_target\_seqsis intentional #422 - query_pan_genome 'Cant access file' error (Non-Working-Directory inputs) #421
- How many .gff files does Roary need? #419
- Installation through Bioconda not working #418
- Is it possible to run roary without prokka output files? #417
- Exiting early because number of clusters is too high #415
- MSG: Got a sequence without letters. Could not guess alphabet? #414
- Which is the advantage to pre-use prokka to perform analysis using genbank (.gbk and gbff) files? #412
- issues with running and empty files #411
- MSG: Got a sequence without letters. Could not guess alphabet #410
- moose.pm issue #407
- Tutorial data: extract_proteome_from_gff #406
- Tutorial data: extract_proteome_from_gff #403
- gene_presence_absence.csv incomplete #402
- Roary including non-protein coding features? #398
- Question: what programs can be used to visualize embl and dot files? #394
- Roary Does not terminated successfully #388
- python: can't open file 'roary_plots.py': [Errno 2] No such file or directory #385
- Roary does not finish analysis even though cluster job queue returns successful completion #383
- Genes (well) annotated in prokka end up all in different groups?? #355
- could not determine version of cd-hit #322
- Use of uninitialized value in require at (eval 792) line 1. #308
- Error: unexpected input in "_" #299
- inconsistent referencing of $TMPDIR ? #287
Merged pull requests:
- Include tests in README #430 (ssjunnebo)
- 621556 badges #420 (ssjunnebo)
- Update roary_plots from .ix to .loc #416 (EvdH0)
- Use only CDS features from GFF #400 (embatty)
- also mention Devel::OverloadInfo and Digest::MD5::File as required Perl dependencies #397 (boegel)
- Avoid deprecation errors in roary_plots #389 (mgalardini)
v3.12.0 (2018-01-23)
Merged pull requests:
v3.11.4 (2018-01-16)
Closed issues:
- Roary seemed to have stopped prematurely; any way to continue the run? #380
- Getting prank version without the online check #377
- Kraken version parsing error: #376
- 3.11.1 failing 2/55 (3/791) tests #375
- Fix for prank version check #361
- mafft version check still failing - bug in regexp found #360
- roary -a => Use of uninitialized value in concatenation (.) #270
Merged pull requests:
- Fix dependancy checking option #382 (andrewjpage)
v3.11.3 (2018-01-12)
Merged pull requests:
- Version fix #379 (andrewjpage)
v3.11.2 (2018-01-12)
Fixed bugs:
- ExtractProteomeFromGff.t failing tests 3.11.0 #373
Merged pull requests:
- fix mafft and kraken version extraction #378 (andrewjpage)
v3.11.1 (2018-01-10)
Closed issues:
- Sorting in version 3.11.0: uppercase letters first, lowercase second (non-alphabetical) #371
- Genbank input #365
- not all annotated features are allocated to the clusters #359
Merged pull requests:
- Bedtools getfasta format fix #374 (andrewjpage)
- Update roary_plots.py #372 (franz89)
- Issue #363 add check for duplicate basenames #370 (nickp60)
- README.md: Update Guix install instructions. #362 (wwood)
v3.11.0 (2017-10-10)
Fixed bugs:
- Can't get version of kraken, kraken-report or mafft ? #312
Closed issues:
Merged pull requests:
- change missing gene in core to be dashes rather than Ns #358 (andrewjpage)
v3.10.2 (2017-09-08)
Closed issues:
- [version 3.8.0] Roary crashes at end on perl error message #323
- Cant open file: _accessory_clusters.clstr #320
Merged pull requests:
- get kraken version #351 (andrewjpage)
v3.10.1 (2017-09-07)
Implemented enhancements:
Fixed bugs:
- The GNU General Public License, Version not specified #344
Closed issues:
- MSG: The sequence does not appear to be FASTA format (lacks a descriptor line '>') #346
Merged pull requests:
- Improve input file handling #350 (andrewjpage)
v3.10.0 (2017-09-07)
Closed issues:
- Use of uninitialized value (Perl) #345
- identical .gff file names from different genome, and then issue with mcl groups #341
- Cant open file: _clustered.clstr #339
v3.9.1 (2017-08-22)
Merged pull requests:
- Optionally allow paralogs in core gene alignment #343 (andrewjpage)
- Script to find frequency of unique genes in samples #340 (andrewjpage)
v3.9.0 (2017-08-09)
Closed issues:
- roary_plots: pangenome matrix tree does not look like input.newick tree #333
- use Roary with RAST files #332
- Roary #329
- sampling number is 10 in number of genes in pan and core genome #319
Merged pull requests:
- Grammar edits #327 (cgreene)
- allow for inflation factor for MCL to be changed #326 (andrewjpage)
v3.8.2 (2017-05-21)
v3.8.1 (2017-05-21)
Closed issues:
- BLAST Database error #321
- Results for same input differ always a bit (summary_statistics.txt) #318
- Error: Couldnt open GFF file #314
- Help with query_pan_genome #313
Merged pull requests:
- update email address #325 (ssjunnebo)
- New option to roary_plots.py #317 (mgalardini)
v3.8.0 (2017-01-25)
Closed issues:
- Old version in the master tarball? #300
- prank is not installed (Linuxbrew) #294
- roary_plots.py problem #292
Merged pull requests:
- Support latest version of blast #306 (andrewjpage)
- infgen #305 (andrewjpage)
- update from 108 to 118 #304 (andrewjpage)
- update usage text for iterative CD-hit #301 (andrewjpage)
v3.7.1 (2016-11-01)
Closed issues:
Merged pull requests:
- fix spelling #280 (satta)
- dont add POD to end of R scripts #279 (andrewjpage)
v3.7.0 (2016-09-23)
v3.6.9 (2016-09-22)
Implemented enhancements:
Closed issues:
- roary_plots.py missing #277
- Errors when downloaded sequences from NCBI #274
- Same dataset different results! #271
- _clustered.clstr file does not exist, cannot be read #250
Merged pull requests:
- Fixed easy-init warnings - 529655 #278 (psweston)
- README.md: Add instructions for GNU Guix. #273 (wwood)
v3.6.8 (2016-08-02)
Merged pull requests:
- Allow gene names from gb #266 (andrewjpage)
- Missing genes #265 (andrewjpage)
v3.6.7 (2016-07-26)
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
- roary R plots don't work on server --- lack of X11 #194
Closed issues:
- empty accessory_binary_genes.fa file #262
- a guix package #259
- create_pan_genome_plots.R - X11 font problem #230
- Roary not generating pan_genome_reference.fa #223
- Roary not using packaged executables #215
v3.6.6 (2016-07-25)
Fixed bugs:
- GFF parsing doesn't match GFF3 specification #249
Merged pull requests:
- Fix empty accessory binary #264 (andrewjpage)
- change to dist zilla starter bundle #261 (nds)
v3.6.5 (2016-07-20)
Merged pull requests:
- allow new format bedtools and dont look for FASTA in GFF #260 (andrewjpage)
- catch divide by zero error #258 (andrewjpage)
v3.6.4 (2016-07-06)
Merged pull requests:
- drop testing for perl 5.10, add 5.24. dzil no longer works below 5.14 #257 (andrewjpage)
v3.6.3 (2016-07-01)
Merged pull requests:
- Speed up alignments #256 (andrewjpage)
v3.6.2 (2016-05-10)
Implemented enhancements:
- Prefix utility commands with roary- ? #226
Merged pull requests:
- fix bug Can't exec /bin/sh: Argument list too long #247 (duytintruong)
- get rid of warning message #246 (satta)
v3.6.1 (2016-04-18)
Fixed bugs:
- roary_plots.py generating flawed plots #221
Closed issues:
- Core gene file missing error #241
Merged pull requests:
- prefix commands with roary #244 (andrewjpage)
- More improvements to roary_plots #240 (mgalardini)
v3.6.0 (2016-02-23)
Fixed bugs:
- MSG: Got a sequence without letters. Could not guess alphabet #229
Closed issues:
- Roary 3.5.8 works with -i 80 switch, but not with -i 90 or higher with large datasets? #234
- How to use multiple switches in commandline? #232
Merged pull requests:
- Improvements to roary_plots #236 (mgalardini)
- Rollback 3 5 8 #235 (andrewjpage)
v3.5.9 (2016-02-17)
Implemented enhancements:
- What clusters end up in gene accessory_binary_genes.fa ? #225
Closed issues:
- roary.github.io just prints HELLO #233
Merged pull requests:
v3.5.8 (2016-01-20)
Implemented enhancements:
- Getting Roary into Debian Med #219
- Add embl output file mapping location of each core gene in the core genome alignment #192
Closed issues:
- Error message: Cannot find the mcxdeblast executable, please ensure its in your PATH #217
Merged pull requests:
- Provide full accessory for building binary tree #227 (andrewjpage)
- roary_plots: new fields in roary output must be parsed away #222 (mgalardini)
- Debian nitpicks #220 (satta)
- Core alignment header file #218 (andrewjpage)
v3.5.7 (2015-12-17)
Closed issues:
- Roary not checking tools needed to run #214
Merged pull requests:
- Core gene count #213 (andrewjpage)
v3.5.6 (2015-12-01)
Implemented enhancements:
- Non-issue, FYI regarding my 'roary2svg.pl' script #195
Merged pull requests:
- add roary2svg script #212 (andrewjpage)
v3.5.5 (2015-11-26)
Merged pull requests:
- CD-hit threads limit #211 (andrewjpage)
v3.5.4 (2015-11-26)
Fixed bugs:
- Use of uninitialized value in require at (eval ..) line 1. #204
- [bug] Newick files in 3.5.1 have branch lengths of 0.0 #202
Merged pull requests:
- Accessory binary fasta contains all C's fix #210 (andrewjpage)
v3.5.3 (2015-11-26)
Implemented enhancements:
- Enhancement: roary -a to continue on if other parameters as well #207
- Make summary_statistics a TAB/TSV file? #193
Fixed bugs:
v3.5.2 (2015-11-25)
Fixed bugs:
- Use of uninitialized value in File::Slurper and Encode.pm #196
Merged pull requests:
- Improved dependancy checking #209 (andrewjpage)
- Lsf update gene alignments #201 (andrewjpage)
v3.5.1 (2015-11-12)
Fixed bugs:
- Accessory genes newick file contains full path of infividual files #200
- add optional dependancy from File::Slurper to stop warnings being printed #199 (andrewjpage)
v3.5.0 (2015-11-12)
Merged pull requests:
- remove path from accessory tree #198 (andrewjpage)
v3.4.3 (2015-11-11)
Merged pull requests:
- consensus group name for pan reference #190 (andrewjpage)
v3.4.2 (2015-10-12)
Merged pull requests:
- Gene presence and absence rtab #189 (andrewjpage)
v3.4.1 (2015-10-08)
Implemented enhancements:
- Need protein lengths in the final spreadsheet #116
Fixed bugs:
- Bio-RetrieveAssemblies-1.0.1 fails to install #151
Merged pull requests:
v3.4.0 (2015-10-07)
Merged pull requests:
- Extra columns in spreadsheet with gene lengths #186 (andrewjpage)
v3.3.4 (2015-10-07)
Closed issues:
- EXCEPTION: Bio::Root::Exception could not read ...faa.intermediate.extracted.fa #175
Merged pull requests:
- increase dependancy RAM #185 (andrewjpage)
- Use lsf for gene alignment #184 (andrewjpage)
v3.3.3 (2015-09-29)
Merged pull requests:
- dont align if sequences same length and nearly the same #183 (andrewjpage)
v3.3.2 (2015-09-28)
Implemented enhancements:
- Use of temporary folders and files #177
Merged pull requests:
- Duplicate sequences in pan genome reference fasta #182 (andrewjpage)
v3.3.1 (2015-09-25)
Merged pull requests:
- Fix usage text #181 (andrewjpage)
v3.3.0 (2015-09-24)
Fixed bugs:
- Check at least 2 gff files have been passed in #171
- Pentuple memory for worst case sCenario #170
- 00_requires_external.t missing "mafft" ? #168
Merged pull requests:
- Check dependancies #180 (andrewjpage)
v3.2.9 (2015-09-23)
Implemented enhancements:
- Add --outdir option to avoid blatting current directory #176
Fixed bugs:
- CPAN install failure "unknown option mafft" #169
Closed issues:
- Error "Cant open file: _uninflated_mcl_groups" #179
Merged pull requests:
- Add the option to specify an output directory #178 (andrewjpage)
v3.2.8 (2015-09-23)
v3.2.7 (2015-09-02)
Merged pull requests:
- count paralogs correctly when looking for differences in datasets #174 (andrewjpage)
v3.2.6 (2015-09-02)
Merged pull requests:
- revert core tree generation #173 (andrewjpage)
v3.2.5 (2015-08-17)
Merged pull requests:
- Verbose stats #172 (andrewjpage)
- dont set bioperl version #167 (andrewjpage)
v3.2.4 (2015-07-23)
Merged pull requests:
- update readme citation #165 (andrewjpage)
v3.2.3 (2015-07-22)
Merged pull requests:
- update citation message #164 (andrewjpage)
- Pass mafft through to alignment #163 (andrewjpage)
v3.2.1 (2015-07-21)
v3.2.0 (2015-07-20)
Merged pull requests:
- Use mafft #162 (andrewjpage)
- output summary file #161 (andrewjpage)
- Pass through dont delete flag #160 (andrewjpage)
- Assembly statistics #159 (andrewjpage)
v3.1.2 (2015-07-13)
3.1.2 (2015-07-13)
Fixed bugs:
- prank seg fault #157
Merged pull requests:
- Core gene missing files #158 (andrewjpage)
v3.1.1 (2015-06-26)
Closed issues:
- sadaf #154
v3.1.0 (2015-06-22)
Merged pull requests:
- Accessory binary tree #155 (andrewjpage)
v3.0.3 (2015-06-15)
Fixed bugs:
- Annotation missing in set_difference_unique_set_one/two_statistics.csv files #137
Merged pull requests:
- when creating core gene alignment, lookup sample names to genes in sp… #153 (andrewjpage)
- Only align core files #150 (andrewjpage)
v3.0.2 (2015-06-12)
Implemented enhancements:
- Print out the version number #119
Merged pull requests:
- Mafft and exonerate dependancies #149 (andrewjpage)
- Add a version parameter and add in marcos plots code #148 (andrewjpage)
v3.0.1 (2015-06-12)
Fixed bugs:
- Use of -e switch gives multifasta file with N's only #132
v3.0.0 (2015-06-11)
Merged pull requests:
- Use prank for core genome alignments #147 (andrewjpage)
- Accessory graph #146 (andrewjpage)
v2.3.4 (2015-06-10)
v2.3.3 (2015-06-08)
Merged pull requests:
- Simplify perl dependency installation #145 (bewt85)
- Pan genome reference #144 (andrewjpage)
- Fix input files with duplicate IDs #143 (andrewjpage)
- Test against different versions of GNU Parallel #142 (bewt85)
v2.3.2 (2015-06-08)
Fixed bugs:
- GFF files derived from Prokka genbank raise errors #130
- MSG: Got a sequence without letters. Could not guess alphabet #127
Merged pull requests:
- TravisCI only wants the major and minor version of perl #141 (bewt85)
- Add TravisCI support #140 (bewt85)
- Use locus tag when ID is missing from GFF #139 (andrewjpage)
v2.3.1 (2015-06-02)
Merged pull requests:
- Extract IDs from GFF file using Bio::Perl #138 (andrewjpage)
v2.3.0 (2015-06-01)
Closed issues:
- "cpan" command reports Bio::Roary as version '(undef)' #134
v2.2.6 (2015-06-01)
Closed issues:
Merged pull requests:
- include version numbers for cpan #136 (andrewjpage)
- New version number for contributed fix for issue #128 #135 (andrewjpage)
- gnu parallel switch for ubuntu #131 (andrewjpage)
- Backward compatible deferencing of hashes #129 (mgalardini)
v2.2.4 (2015-05-29)
Closed issues:
Merged pull requests:
- Cleanup files #126 (andrewjpage)
v2.2.3 (2015-05-21)
Closed issues:
Merged pull requests:
- Update Kraken QC #125 (andrewjpage)
v2.2.2 (2015-05-21)
Closed issues:
- Hard-coded Sanger paths in some scripts #124
- You're missing some Perl dependancies #123
- Add support for GFF files from NCBI #120
Merged pull requests:
- Fix usage text #122 (andrewjpage)
v2.2.0 (2015-05-14)
Closed issues:
- Verbose output with -v #113
Merged pull requests:
- Accept genbank files #121 (andrewjpage)
v2.1.2 (2015-05-12)
Merged pull requests:
- Verbose output #118 (andrewjpage)
v2.1.1 (2015-04-29)
Merged pull requests:
- pass core definition into number of conserved genes plot #111 (andrewjpage)
- Vary core definition #110 (andrewjpage)
- Use block quotes in readme #109 (bewt85)
v2.0.9 (2015-04-20)
Merged pull requests:
- Allow for multiple processors to be used #108 (andrewjpage)
v2.0.8 (2015-04-09)
Merged pull requests:
- Speedup #107 (andrewjpage)
- new version 2.0.7 #106 (andrewjpage)
v2.0.7 (2015-03-28)
Merged pull requests:
- old splits #105 (andrewjpage)
- Speedup split #104 (andrewjpage)
v2.0.5 (2015-03-26)
Merged pull requests:
- Stop deep recursion #103 (andrewjpage)
- check programs installed #102 (andrewjpage)
2.0.4 (2015-03-23)
Merged pull requests:
- File slurp tiny #101 (andrewjpage)
- version 2.0.3 #100 (andrewjpage)
2.0.3 (2015-03-17)
Merged pull requests:
- Remove LSF support #99 (andrewjpage)
- Dont set LSF as the default runner #98 (andrewjpage)
- Rename directories to Roary #97 (andrewjpage)
v2.0.0 (2015-03-16)
Merged pull requests:
- Ship binaries #96 (andrewjpage)
- Pad merged multifastas when data is missing #95 (carlacummins)
- Subsample reads #94 (andrewjpage)
- Merge Carlas CGN #93 (andrewjpage)
- rename spreadsheet #92 (andrewjpage)
- Refactor out fasta grep #91 (andrewjpage)
- remove fasta_grep #90 (andrewjpage)
- Add gnu parallel support #89 (andrewjpage)
- Updated create_pan_genome help text to include -qc option #88 (carlacummins)
- QC report option added #87 (carlacummins)
- increase blastp min memory to 3gb from 100 #86 (andrewjpage)
- Remove fastatranslate dependancy #85 (andrewjpage)
- Queue set to basement if number of samples > 600 (previously 800) #84 (carlacummins)
- Bug fix #83 (carlacummins)
- Added verbose stats option #82 (carlacummins)
- Group limit changed to 50,000 #81 (carlacummins)
- Multifastas not created when group limit (default 8000) exceeded #80 (carlacummins)
- allow for translation table to be passed in #79 (andrewjpage)
- increase memory #78 (andrewjpage)
- Allow user specify sorting when reordering spreadsheet against a tree #77 (andrewjpage)
- Bug fixing #76 (carlacummins)
- Added AUTHORS file #75 (aslett1)
- if theres more than 1k samples use basement for default analysis #74 (andrewjpage)
- use long queue for more than 200 samples #73 (andrewjpage)
- core alignment gets run with lsf #72 (andrewjpage)
- Job runner ids lsf #71 (andrewjpage)
- Core alignment missing file #70 (andrewjpage)
- Core alignment missing file #69 (andrewjpage)
- update error reporting #68 (andrewjpage)
- Create core alignment from spreadsheet and multifasta files #67 (andrewjpage)
- make script executable #66 (andrewjpage)
- script to merge multifasta files together #65 (andrewjpage)
- rename output gene multfastas and pass all sequences through #64 (andrewjpage)
- Align genes at protein level and back translate to nucleotides #63 (andrewjpage)
- Depth first search for reordering spreadsheet #62 (andrewjpage)
- make the iterative cdhit script useful for standalone use #61 (andrewjpage)
- query_pan_genome_update_text #60 (andrewjpage)
- fix failing tests #59 (andrewjpage)
- Create plot for % blast identity #58 (andrewjpage)
- add a flag to keep intermediate files #57 (andrewjpage)
- set the known gene names to black and rest to colours #56 (andrewjpage)
- print fragment blocks #55 (andrewjpage)
- Fix ordering of accessory #54 (andrewjpage)
- fix r plots #53 (andrewjpage)
- Overlapping proteins #52 (andrewjpage)
- Gene order #51 (andrewjpage)
- pass job runner to iterative cdhit #50 (andrewjpage)
- iterative cdhit in a job #49 (andrewjpage)
- Fix tests #48 (andrewjpage)
- Prefilter optimisation #47 (andrewjpage)
- dont split groups #46 (andrewjpage)
- rename create plots R script #45 (andrewjpage)
- cdhit should output full description of sequence name #44 (andrewjpage)
- Gene count plot #43 (andrewjpage)
- align gene multifasta files using muscle #42 (andrewjpage)
- Reorder spreadsheet #41 (andrewjpage)
- Reorder spreadsheet #40 (andrewjpage)
- Speedup post analysis #39 (andrewjpage)
- Presence and absence of genes #38 (andrewjpage)
- split big groups based on annotation #37 (andrewjpage)
- make multifasta files easier to sort #36 (andrewjpage)
- dont wait in lfs scheduler #35 (andrewjpage)
- run post analysis as a job #34 (andrewjpage)
- annotate the names of the groups files #33 (andrewjpage)
- Output all sequences making up pan genome in multifasta files #32 (andrewjpage)
- Run external applications through lsf #31 (andrewjpage)
- remove done dependancy job #30 (andrewjpage)
- blocking job #29 (andrewjpage)
- Filter unknowns in LSF jobs #28 (andrewjpage)
- Pass job runner through to extract gffs #27 (andrewjpage)
- Change case of GFF commandline class #26 (andrewjpage)
- use LSF to do the inital parsing of input files #25 (andrewjpage)
- renamed LICENSE #24 (CraigPorter)
- GPL #23 (andrewjpage)
- lsf memory in mb #22 (andrewjpage)
- low complexity filtering #21 (andrewjpage)
- inflate clusters where the representative gene is not the first #20 (andrewjpage)
- report more sequences from blastp #19 (andrewjpage)
- update tests for different input processing #18 (andrewjpage)
- speedup extracting proteins from gff #17 (andrewjpage)
- sort spreadsheet by number of isolates #16 (andrewjpage)
- create spreadsheets of differences between sets #15 (andrewjpage)
- Output statistics on groups #14 (andrewjpage)
- Find the difference between isolates #13 (andrewjpage)
- check if group is null #12 (andrewjpage)
- catch undef #11 (andrewjpage)
- tests for create pan genome script #10 (andrewjpage)
- label fasta sequences with annotation ID #9 (andrewjpage)
- extract proteomes from gffs and transfer anntotation as part of script #8 (andrewjpage)
- transfer annotation #7 (andrewjpage)
- speedup searching fastas #6 (andrewjpage)
- typo in memory estimation #5 (andrewjpage)
- run mcl and inflate results #4 (andrewjpage)
- vary memory usage according to input file size #3 (andrewjpage)
- working on real data #2 (andrewjpage)
- Initial functionality #1 (andrewjpage)