| c335b7a | Torsten Seemann | 04 August 2020, 04:10:03 UTC | Merge pull request #513 from smsaladi/patch-1 fix typos in README.md | 04 August 2020, 04:10:03 UTC |
| fc6d822 | Shyam Saladi | 04 August 2020, 04:07:05 UTC | fix typo | 04 August 2020, 04:07:05 UTC |
| f9ce4e3 | Shyam Saladi | 04 August 2020, 04:05:13 UTC | fix typos | 04 August 2020, 04:05:13 UTC |
| 9c428c4 | Anders Goncalves da Silva | 03 August 2020, 22:16:06 UTC | Add code of conduct | 03 August 2020, 22:16:06 UTC |
| b3fe5c8 | Torsten Seemann | 13 May 2020, 19:48:10 UTC | Merge pull request #489 from telatin/patch-1 missing -r operator in checking indexes | 13 May 2020, 19:48:10 UTC |
| 5b58020 | Andrea Telatin | 13 May 2020, 19:01:36 UTC | missing -r operator in checking indexes Lack of `HAMAP.hmm.h3i` not detected unless adding -r | 13 May 2020, 19:01:36 UTC |
| 04df7b3 | Torsten Seemann | 20 February 2020, 05:12:25 UTC | Bump version 1.14.6 | 20 February 2020, 05:12:25 UTC |
| edc839a | Torsten Seemann | 20 February 2020, 03:53:21 UTC | travis: use bionic / ubuntu 18 | 20 February 2020, 03:53:21 UTC |
| c13fce7 | Torsten Seemann | 20 February 2020, 03:49:23 UTC | travis: try system perl | 20 February 2020, 03:49:23 UTC |
| 09d6e5d | Torsten Seemann | 20 February 2020, 03:40:05 UTC | travis: try .deb instead of cpanm | 20 February 2020, 03:40:05 UTC |
| bd6a258 | Torsten Seemann | 20 February 2020, 03:29:52 UTC | travis: add Bio::SearchIO::hmmer | 20 February 2020, 03:29:52 UTC |
| 4140ada | Torsten Seemann | 20 February 2020, 02:39:49 UTC | travis: cpanm whole bio::perl | 20 February 2020, 02:39:49 UTC |
| e680fe9 | Torsten Seemann | 20 February 2020, 02:33:51 UTC | travis: add apt libdb-dev | 20 February 2020, 02:33:51 UTC |
| 4dd164f | Torsten Seemann | 19 February 2020, 01:11:49 UTC | Add docker/singularity instructions | 19 February 2020, 01:11:49 UTC |
| 290466d | Torsten Seemann | 23 January 2020, 02:56:52 UTC | travis: test with perl 5.30 | 23 January 2020, 02:56:52 UTC |
| 1adb68b | Torsten Seemann | 23 January 2020, 01:29:20 UTC | travis: install bioperl module by module | 23 January 2020, 02:29:06 UTC |
| 8c82891 | Torsten Seemann | 23 January 2020, 00:02:30 UTC | Update tbl2asn 25.8 binaries | 23 January 2020, 00:02:30 UTC |
| 4d6894d | Torsten Seemann | 11 November 2019, 07:49:19 UTC | Bump to 1.14.5 | 11 November 2019, 07:49:19 UTC |
| ece558a | Torsten Seemann | 11 November 2019, 07:29:45 UTC | Add --prodigaltf to docs | 11 November 2019, 07:31:19 UTC |
| 9e57acc | Torsten Seemann | 11 November 2019, 07:21:21 UTC | Ensure barrnap version check has locale C | 11 November 2019, 07:21:21 UTC |
| 7d86e4e | Torsten Seemann | 11 November 2019, 07:18:16 UTC | FAQ question for sequence-less GFF | 11 November 2019, 07:18:16 UTC |
| bec35e7 | Torsten Seemann | 11 November 2019, 07:01:54 UTC | Merge pull request #269 from ucpete/ucpete-parent-first Parents written to GFF before children | 11 November 2019, 07:01:54 UTC |
| d47de0e | Torsten Seemann | 11 November 2019, 06:51:59 UTC | Issue #429 | add --prodigaltf option | 11 November 2019, 06:51:59 UTC |
| 737af7f | Torsten Seemann | 11 November 2019, 06:42:06 UTC | Issue #425 | Remove legacy --docs option | 11 November 2019, 06:42:36 UTC |
| a8707d3 | Torsten Seemann | 11 November 2019, 05:33:19 UTC | Update HAMAP database | 11 November 2019, 05:33:19 UTC |
| 1cc182a | Torsten Seemann | 11 November 2019, 03:08:53 UTC | Issue #435 | handle BLAST 2.10 ver compare | 11 November 2019, 05:23:39 UTC |
| 4ba3b33 | Torsten Seemann | 21 October 2019, 07:41:26 UTC | Update sprot DBs to Release 2019_09 | 11 November 2019, 05:20:18 UTC |
| 1d9901c | Torsten Seemann | 21 October 2019, 06:36:13 UTC | Ignore BLAST+ indices | 21 October 2019, 06:36:13 UTC |
| a525082 | Torsten Seemann | 11 October 2019, 04:39:31 UTC | Issue #422 - document AMR+IS annotations & update AMR | 11 October 2019, 04:44:52 UTC |
| 70b8ac1 | Torsten Seemann | 03 October 2019, 07:04:29 UTC | Merge pull request #186 from peterjc/patch-2 EMBL validator moved (also now versioned) | 03 October 2019, 07:04:29 UTC |
| 6ce5504 | Torsten Seemann | 03 October 2019, 06:55:33 UTC | badge formatting | 03 October 2019, 06:55:33 UTC |
| 2677236 | Torsten Seemann | 03 October 2019, 06:53:08 UTC | fix apostrophe's PR #206 | 03 October 2019, 06:53:08 UTC |
| 6239420 | Torsten Seemann | 03 October 2019, 06:51:34 UTC | Merge pull request #355 from nsoranzo/patch-1 Remove deprecated ``sudo: false`` from .travis.yml | 03 October 2019, 06:51:34 UTC |
| 286d97a | Torsten Seemann | 03 October 2019, 06:42:28 UTC | bump version cf signalp 5 PR | 03 October 2019, 06:42:28 UTC |
| 4729534 | Torsten Seemann | 03 October 2019, 06:40:23 UTC | Merge pull request #418 from ealdraed/feature/SignalP-5.0 Add support for SignalP-5.0 | 03 October 2019, 06:40:23 UTC |
| eecec30 | ealdraed | 30 September 2019, 11:01:30 UTC | Add support for SignalP-5.0 | 30 September 2019, 11:01:30 UTC |
| 319ef8b | Torsten Seemann | 23 September 2019, 12:09:05 UTC | Issue #413 | update manual.txt | 23 September 2019, 12:09:05 UTC |
| 6e380ba | Torsten Seemann | 08 September 2019, 08:02:08 UTC | Merge pull request #407 from bioforensics/rfam-update Update Rfam covariance models and cmscan command | 08 September 2019, 08:02:08 UTC |
| 6b2bd73 | Torsten Seemann | 08 September 2019, 07:13:43 UTC | Issue #348 | uniq on dupes in --listdb | 08 September 2019, 07:13:43 UTC |
| c7f9c2f | Torsten Seemann | 08 September 2019, 07:04:42 UTC | Issue #379 | temp file clash w/ same --outdir / diff --prefix | 08 September 2019, 07:04:42 UTC |
| bcb11ba | Daniel Standage | 15 August 2019, 17:51:47 UTC | Filter out matches that overlap with a higher scoring match (https://rfam.readthedocs.io/en/latest/genome-annotation.html#removing-lower-scoring-overlaps-from-a-tblout-file) | 15 August 2019, 17:51:47 UTC |
| 70ce674 | Daniel Standage | 15 August 2019, 15:34:33 UTC | Use --fmt 2 and adjust output parsing as suggested by @ealdraed | 15 August 2019, 15:34:33 UTC |
| c0c3963 | Daniel Standage | 14 August 2019, 17:38:10 UTC | Fix cutoff options, update CM README | 14 August 2019, 17:38:10 UTC |
| 8b7763a | Daniel Standage | 14 August 2019, 16:25:38 UTC | Update Rfam covariance models to 14.1 | 14 August 2019, 16:25:38 UTC |
| 17d9534 | Torsten Seemann | 09 August 2019, 05:14:38 UTC | Bump to 1.14.0 | 09 August 2019, 05:14:38 UTC |
| ee72b53 | Torsten Seemann | 09 August 2019, 05:14:08 UTC | Add BREWCONDA placeholder in each perl script | 09 August 2019, 05:14:08 UTC |
| 85a036c | Torsten Seemann | 09 August 2019, 05:12:03 UTC | Update tbl2asn to 25.7 | 09 August 2019, 05:12:03 UTC |
| 3e7c046 | Torsten Seemann | 18 July 2019, 00:01:58 UTC | Add -c defaults to conda install | 18 July 2019, 00:01:58 UTC |
| 68cf107 | Torsten Seemann | 14 July 2019, 23:14:52 UTC | Reduce length of seq name | 14 July 2019, 23:14:52 UTC |
| 728179f | Torsten Seemann | 29 May 2019, 09:09:42 UTC | Update BLAST+ binaries to 2.9 | 29 May 2019, 09:09:42 UTC |
| 558963e | Torsten Seemann | 29 May 2019, 08:45:38 UTC | Issue #359: random dict order in .txt | 29 May 2019, 08:45:38 UTC |
| 53665ae | Torsten Seemann | 29 May 2019, 08:37:12 UTC | Require BLAST+ >=2.8 for -qcov_hsp_perc | 29 May 2019, 08:37:12 UTC |
| f81a51f | Torsten Seemann | 26 May 2019, 23:05:17 UTC | Issue #387 | Fix --version mismatch | 26 May 2019, 23:05:17 UTC |
| a52a8b0 | Torsten Seemann | 15 April 2019, 22:15:08 UTC | Merge pull request #378 from robymetallo/master Updated grep and regexp to fix bug when detecting parallel version | 15 April 2019, 22:15:08 UTC |
| cf0be46 | Roberto Rossini | 13 April 2019, 22:54:11 UTC | Updated grep and regexp to detect parallel version | 13 April 2019, 22:54:11 UTC |
| 568b7e1 | Torsten Seemann | 17 December 2018, 03:53:43 UTC | Update tbl2asn binaries | 17 December 2018, 03:53:43 UTC |
| 97bc1ac | Nicola Soranzo | 06 December 2018, 19:13:24 UTC | Remove deprecated ``sudo: false`` from .travis.yml See https://blog.travis-ci.com/2018-11-19-required-linux-infrastructure-migration | 06 December 2018, 19:13:24 UTC |
| 88c99bf | Torsten Seemann | 04 September 2018, 08:17:14 UTC | Fix typo in 'tranposase' doh... | 04 September 2018, 08:17:14 UTC |
| ce71448 | Torsten Seemann | 01 September 2018, 05:23:23 UTC | Issue #333 | add perl5 badge | 01 September 2018, 05:23:23 UTC |
| a09502e | Torsten Seemann | 01 September 2018, 04:33:45 UTC | Issue #258 | add ISFinder/AMR support, custom evalue, --coverage | 01 September 2018, 04:33:45 UTC |
| 76f1371 | Torsten Seemann | 01 September 2018, 01:08:26 UTC | Issue #332 | reinstate CRISPR features, minced 0.3 | 01 September 2018, 01:08:26 UTC |
| 2f93240 | Torsten Seemann | 31 August 2018, 01:38:02 UTC | Issue #328 | COG, it's db_xref not dbxref | 31 August 2018, 01:38:02 UTC |
| be7aef5 | Torsten Seemann | 25 August 2018, 03:57:22 UTC | Issue #328 | remove ilegal score tag for crispr | 25 August 2018, 03:57:22 UTC |
| 099889b | Torsten Seemann | 06 August 2018, 01:17:41 UTC | Add DOI badge for Prokka paper | 06 August 2018, 01:17:41 UTC |
| 9afe26a | Torsten Seemann | 31 May 2018, 03:55:10 UTC | Ensure --dbdir is set before list_db() etc | 31 May 2018, 03:55:10 UTC |
| 36e54ea | Torsten Seemann | 31 May 2018, 03:01:14 UTC | Issue #312 | add --dbdir / $PROKKA_DBDIR | 31 May 2018, 03:01:14 UTC |
| 466ee4f | Torsten Seemann | 31 May 2018, 03:00:51 UTC | Use newer perl on travis | 31 May 2018, 03:00:51 UTC |
| 795abf1 | Torsten Seemann | 28 May 2018, 09:31:25 UTC | Issue #297 | Fix conda-forge / bioconda order | 28 May 2018, 09:31:25 UTC |
| e311f47 | Torsten Seemann | 26 May 2018, 23:34:19 UTC | Fix wrong brew install repo | 26 May 2018, 23:34:19 UTC |
| a8c8fd4 | Torsten Seemann | 26 May 2018, 23:33:41 UTC | Minor typo in comment | 26 May 2018, 23:33:41 UTC |
| 60eb591 | Torsten Seemann | 28 March 2018, 23:52:00 UTC | Fix conda install instructions (Issue #295) | 28 March 2018, 23:52:00 UTC |
| d6adb2c | Torsten Seemann | 27 March 2018, 00:13:00 UTC | Remove broken bundled Perl modules | 27 March 2018, 00:13:00 UTC |
| 545e1ab | Torsten Seemann | 25 March 2018, 06:22:01 UTC | Put module search path before 'use' | 25 March 2018, 06:22:01 UTC |
| 026f742 | Torsten Seemann | 25 March 2018, 05:46:01 UTC | bump to 1.13 | 25 March 2018, 05:46:01 UTC |
| ff2efa6 | Torsten Seemann | 24 March 2018, 04:54:20 UTC | Add GPLv3 info | 24 March 2018, 04:54:20 UTC |
| 7842dd5 | Torsten Seemann | 24 March 2018, 04:49:14 UTC | Add support for COG annotation | 24 March 2018, 04:49:14 UTC |
| 00a3be3 | Torsten Seemann | 24 March 2018, 02:33:08 UTC | Streamline the docs | 24 March 2018, 02:33:08 UTC |
| 151aaca | Torsten Seemann | 05 March 2018, 07:33:25 UTC | Update NCBI binaries | 05 March 2018, 07:33:25 UTC |
| e720200 | Peter Skewes-Cox | 20 November 2017, 21:26:38 UTC | Parents written to GFF before children It is commonplace (but neither required, nor specification) for parent features (e.g. `gene`) to precede their child features (e.g. `CDS`) in GFF files. This branch tweaks the sorting of features before writing to GFF, such that parent features are written before their children. Note that this is only applicable when `--addgenes` or `--addmrna` are invoked, and this change is purely cosmetic. | 20 November 2017, 21:26:38 UTC |
| 12547ca | Torsten Seemann | 14 September 2017, 02:51:15 UTC | cleaning up of README markdown | 14 September 2017, 02:51:15 UTC |
| 60bb9f4 | Torsten Seemann | 14 September 2017, 02:44:52 UTC | bug: allow clean_db to return to setup_db | 14 September 2017, 02:44:52 UTC |
| 660b5d1 | Torsten Seemann | 14 September 2017, 02:38:16 UTC | travis: remove apt-gets | 14 September 2017, 02:38:16 UTC |
| adebe6c | Torsten Seemann | 14 September 2017, 02:37:11 UTC | Add exit(0) at end of clean_db() | 14 September 2017, 02:37:11 UTC |
| c46a57f | Torsten Seemann | 14 September 2017, 02:34:42 UTC | Proper error codes and filehandles for --help | 14 September 2017, 02:34:42 UTC |
| ba00dab | Torsten Seemann | 14 September 2017, 02:15:51 UTC | travis: initial attempt | 14 September 2017, 02:15:51 UTC |
| 29269b5 | Torsten Seemann | 14 September 2017, 02:15:27 UTC | Add badges to top of README | 14 September 2017, 02:15:27 UTC |
| f162887 | Torsten Seemann | 14 September 2017, 02:11:20 UTC | Test file to run on | 14 September 2017, 02:11:20 UTC |
| 4cacaa5 | Torsten Seemann | 26 August 2017, 03:00:19 UTC | Fix TSV output bug (Issue #250) | 26 August 2017, 03:00:19 UTC |
| f8f8567 | Torsten Seemann | 24 August 2017, 01:48:09 UTC | Merge pull request #255 from PeteHaitch/patch-1 Fix typo in README | 24 August 2017, 01:48:09 UTC |
| c17bae5 | Peter Hickey | 24 August 2017, 01:44:30 UTC | Typo in README | 24 August 2017, 01:44:30 UTC |
| 224a96b | Torsten Seemann | 06 August 2017, 04:51:10 UTC | Resolve #242 | prokka --docs can't find docs | 06 August 2017, 04:51:10 UTC |
| f7f819b | Torsten Seemann | 04 April 2017, 01:43:06 UTC | Another cleanup_product exception (Issue #226) | 04 April 2017, 01:43:06 UTC |
| 68d9463 | Torsten Seemann | 22 March 2017, 01:52:18 UTC | Put spaces after markdown heading # ## ### #### | 22 March 2017, 01:52:18 UTC |
| cf66d1b | Torsten Seemann | 14 March 2017, 07:14:57 UTC | Bump to version 1.12 | 14 March 2017, 07:14:57 UTC |
| 201c184 | Torsten Seemann | 14 March 2017, 07:01:40 UTC | Add RPMs to help people with bioperl on RPM dists | 14 March 2017, 07:01:40 UTC |
| fcd8f12 | Torsten Seemann | 14 March 2017, 06:21:40 UTC | Check that `java` exists for minced | 14 March 2017, 06:21:40 UTC |
| f525ff3 | Torsten Seemann | 14 March 2017, 06:17:34 UTC | Add git/java to install dependencies | 14 March 2017, 06:17:34 UTC |
| 18c8c5a | Torsten Seemann | 13 March 2017, 05:45:40 UTC | Fix perl warning about # comment in qw() | 13 March 2017, 05:45:40 UTC |
| 57c20ef | Torsten Seemann | 13 March 2017, 05:39:33 UTC | Explain what --rawproduct does (Issue #208) | 13 March 2017, 05:39:33 UTC |
| 91b334f | Torsten Seemann | 13 March 2017, 05:26:41 UTC | Fix typo in issues link in docs (Issue #217) | 13 March 2017, 05:26:41 UTC |
