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https://github.com/tseemann/prokka
11 May 2023, 20:13:29 UTC
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Revision Author Date Message Commit Date
77de0da Torsten Seemann 28 November 2015, 06:31:47 UTC Fix Issue #143 - missing EC in GBK output 28 November 2015, 06:31:47 UTC
f6d13c7 Torsten Seemann 28 November 2015, 06:10:11 UTC Bump tbl2asn minimum version to 24.3 28 November 2015, 06:10:11 UTC
05f8e64 Torsten Seemann 28 November 2015, 01:05:21 UTC Fix Issue #142 : allow --hmms to work when binary pressed only 28 November 2015, 01:05:21 UTC
3a2424f Torsten Seemann 30 October 2015, 00:46:25 UTC Add --noanno mode and repurpose --fast for BLAST-only searching 30 October 2015, 00:46:25 UTC
e92232a Torsten Seemann 04 July 2015, 22:54:21 UTC Issue #125 - add total bp of contigs to log 04 July 2015, 22:54:21 UTC
918f5fd Torsten Seemann 29 June 2015, 10:23:24 UTC Update bundled BLAST binaries to 2.2.31+ 29 June 2015, 10:23:24 UTC
2fde50f Torsten Seemann 28 June 2015, 10:04:54 UTC Merge pull request #106 from stephenturner/patch-1 add link to tbl2asn 28 June 2015, 10:04:54 UTC
df64e5e Torsten Seemann 21 June 2015, 03:18:11 UTC Fix Issue #111 - add useful GFF Name tag where possible 21 June 2015, 03:18:11 UTC
ab2b2bd Torsten Seemann 21 June 2015, 02:58:48 UTC Fix Issue #119 - incorrectly putting Parent tag in TBL file 21 June 2015, 02:58:48 UTC
4e04820 Torsten Seemann 21 June 2015, 02:48:36 UTC Issue #117 - version check fails if GREP_OPTIONS has colour in it 21 June 2015, 02:48:36 UTC
df653e0 Torsten Seemann 21 June 2015, 00:38:36 UTC Change aragorn tRNA search to linear mode (Issue #108) 21 June 2015, 00:38:36 UTC
8bb7031 Stephen Turner 04 May 2015, 15:25:31 UTC add link to tbl2asn 04 May 2015, 15:25:31 UTC
b57be69 Torsten Seemann 27 April 2015, 20:17:02 UTC Update tbl2asn 24.3 binaries 27 April 2015, 20:17:02 UTC
7eec96a Torsten Seemann 22 April 2015, 22:43:36 UTC Revert MAXCONTIGNIDLEN to 37 to hell with .GBK file restrictions 22 April 2015, 22:43:36 UTC
dd12d9c Torsten Seemann 19 April 2015, 09:43:00 UTC Update primary BLASTP databases from Uniprot 2015_04 19 April 2015, 09:43:00 UTC
cc605c3 Torsten Seemann 19 April 2015, 08:56:33 UTC Update HAMAP database after big fixes in generation script. 19 April 2015, 08:56:33 UTC
74a8d21 Torsten Seemann 19 April 2015, 04:12:12 UTC Allow partial EC numbers to be included in HAMAP DESC lines 19 April 2015, 04:12:12 UTC
052b00c Torsten Seemann 19 April 2015, 03:54:21 UTC Fix Issue #102 dodgy pseudo tRNA invalid coordinates (@skoren) 19 April 2015, 03:54:21 UTC
399d394 Torsten Seemann 13 April 2015, 08:04:02 UTC Modernise hash-bang line for supporting Perl scripts 13 April 2015, 08:04:02 UTC
5b3876f Torsten Seemann 13 April 2015, 07:59:12 UTC Update Prodigal to 2.6.2 to support /transl_table 25 (Issue #71) 13 April 2015, 07:59:12 UTC
05d09cb Torsten Seemann 13 April 2015, 07:41:59 UTC Issue #81 - save msg() calls in buffer so they all go in LOG file 13 April 2015, 07:45:33 UTC
5fb209e Torsten Seemann 13 April 2015, 07:35:51 UTC Add $0 (prokka exe) to log command output 13 April 2015, 07:45:33 UTC
9d51589 Torsten Seemann 13 April 2015, 07:32:04 UTC Move PATH appendations to before tool checking (Issue #97) 13 April 2015, 07:45:22 UTC
96abd1a Torsten Seemann 13 April 2015, 07:19:29 UTC Use 'cmscan --rfam' option to improve search speed 13 April 2015, 07:19:29 UTC
b970764 Torsten Seemann 13 April 2015, 07:04:13 UTC Make DOI and PMID variables. 13 April 2015, 07:04:13 UTC
6eebb6e Torsten Seemann 13 April 2015, 06:40:21 UTC Issue #98 - upgrade HMMER to 3.1b2 13 April 2015, 06:40:21 UTC
85c9b01 Torsten Seemann 13 April 2015, 06:38:13 UTC Issue #100 - upgrade Infernal to 1.1.1 13 April 2015, 06:38:13 UTC
2214faf Torsten Seemann 13 April 2015, 06:35:20 UTC Issue #99 - upgrade BLAST binaries to 2.2.30+ 13 April 2015, 06:35:20 UTC
59c61d3 Torsten Seemann 13 April 2015, 05:56:18 UTC Issue #91 --list on split xxxxx.NN.pin databases 13 April 2015, 05:56:18 UTC
afca613 Torsten Seemann 12 April 2015, 08:10:05 UTC Bundle Time::* modules to help with issue #82 12 April 2015, 08:10:05 UTC
cf122b8 Torsten Seemann 12 April 2015, 07:56:23 UTC Bundle XML::Simple (issue #83) 12 April 2015, 07:56:23 UTC
dddccbe Torsten Seemann 11 April 2015, 21:57:19 UTC Issue #96 - update expired tbl2asn binaries 11 April 2015, 21:57:19 UTC
c9c8403 Torsten Seemann 11 April 2015, 21:52:27 UTC Issue #93 - when too many contigs for tbl2asn 11 April 2015, 21:52:27 UTC
35733af Torsten Seemann 11 April 2015, 21:44:03 UTC Remove refs to defunct VBC institute 11 April 2015, 21:44:03 UTC
2512ec7 Torsten Seemann 10 March 2015, 00:27:54 UTC APT/yum rules for some of the Perl dependencies 10 March 2015, 00:27:54 UTC
10e45d9 Torsten Seemann 09 March 2015, 21:51:09 UTC Issue #74 - typo in help description 09 March 2015, 21:51:09 UTC
ae1a728 Torsten Seemann 09 March 2015, 21:49:38 UTC Issue #72 fix --proteins help message 09 March 2015, 21:49:38 UTC
e02496f Torsten Seemann 04 March 2015, 22:06:26 UTC Update my personal details since leaving Monash Uni 04 March 2015, 22:06:26 UTC
a7ff93d Torsten Seemann 04 March 2015, 22:03:38 UTC Add E.coli "genus" file based on EcoCyc database (trustworthy) 04 March 2015, 22:03:38 UTC
17a2114 Torsten Seemann 04 March 2015, 22:00:27 UTC Bump to 1.12-beta 04 March 2015, 22:00:27 UTC
ef8a296 Torsten Seemann 04 March 2015, 21:59:01 UTC Fix Issue #80 : need prokka-genbank_to_fasta_db in PATH 04 March 2015, 21:59:01 UTC
ccde69b Torsten Seemann 19 February 2015, 03:33:34 UTC Minor changes to msg text 19 February 2015, 03:33:34 UTC
ae235c9 Torsten Seemann 14 February 2015, 07:15:10 UTC Bump to version 1.11 14 February 2015, 07:15:10 UTC
d210346 Torsten Seemann 14 February 2015, 07:14:52 UTC Remove achievements from TODO list 14 February 2015, 07:14:52 UTC
a74d44d Torsten Seemann 14 February 2015, 07:14:44 UTC Update changelog for 1.11 14 February 2015, 07:14:44 UTC
0dd9028 Torsten Seemann 14 February 2015, 07:14:29 UTC Add new options to manual 14 February 2015, 07:14:29 UTC
60d543e Torsten Seemann 14 February 2015, 06:46:09 UTC Fix #69 missing gene.ID and CDS.Parent in GFF3 output 14 February 2015, 06:46:09 UTC
31efd38 Torsten Seemann 14 February 2015, 06:18:23 UTC Issue #35 added --hmms option, analogous to --proteins but for HMMs not FASTA/BLAST 14 February 2015, 06:18:23 UTC
f6da3dd Torsten Seemann 14 February 2015, 05:52:09 UTC For #13 new --debug mode will not delete the temporary BLAST/HMMER in+out files 14 February 2015, 05:52:09 UTC
c148eb5 Torsten Seemann 14 February 2015, 05:29:20 UTC Minor tweaks to cleanup_product() to help Issue #26 14 February 2015, 05:29:20 UTC
7f76d8d Torsten Seemann 14 February 2015, 05:22:35 UTC Correctly set maximum contig name length to 20 characters for #32 14 February 2015, 05:22:35 UTC
74b6548 Torsten Seemann 14 February 2015, 04:58:46 UTC Resolve #32 and trigger error if contig name is > 38 characters 14 February 2015, 04:58:46 UTC
94d1b05 Torsten Seemann 14 February 2015, 04:41:01 UTC Fix #47 by post-sed on broken tbl2asn .gbf file. 14 February 2015, 04:41:01 UTC
7e8f661 Torsten Seemann 14 February 2015, 04:28:24 UTC Show the cmscan command being run for --rfam 14 February 2015, 04:28:24 UTC
2b0b0d6 Torsten Seemann 14 February 2015, 04:12:09 UTC Fix #25 - ensure HMM exists before trying to scan against it! 14 February 2015, 04:12:09 UTC
1c0e128 Torsten Seemann 14 February 2015, 04:11:42 UTC Add --maxlen option to allow exploration of tiny proteins 14 February 2015, 04:11:42 UTC
7a85518 Torsten Seemann 14 February 2015, 04:06:40 UTC Include 2 good Genus databases (our curated Enterococcus and Staphylococcus) 14 February 2015, 04:06:40 UTC
ba64523 Torsten Seemann 14 February 2015, 04:04:38 UTC Bundle smallest HMM in the git repository 14 February 2015, 04:04:38 UTC
99c7174 Torsten Seemann 14 February 2015, 01:55:02 UTC Preliminary support for translation table 25 (new Prodigal binaries) 14 February 2015, 01:55:02 UTC
2346181 Torsten Seemann 14 February 2015, 01:13:05 UTC Fix issue #54 to use proper codon table for all translate() events 14 February 2015, 01:13:05 UTC
6c5d0b0 Torsten Seemann 14 February 2015, 00:49:14 UTC Fix issue #53 not honouring the --hypo flag 14 February 2015, 00:49:14 UTC
90793ee Torsten Seemann 14 February 2015, 00:33:36 UTC Exit error if both --fast and --proteins enabled 14 February 2015, 00:33:36 UTC
e486733 Torsten Seemann 14 February 2015, 00:07:33 UTC Strip _N suffix from /gene before deduplicating them 14 February 2015, 00:07:33 UTC
5bf8647 Torsten Seemann 13 February 2015, 23:45:16 UTC Try different ID tags in .gbk files when making a fasta db 13 February 2015, 23:45:16 UTC
9c1bb70 Torsten Seemann 13 February 2015, 23:29:07 UTC Message detailing each /gene that was de-duplicated. 13 February 2015, 23:29:07 UTC
1db7861 Torsten Seemann 13 February 2015, 07:48:43 UTC Keep order of original contigs in GBK/GFF output files (Fix #46) 13 February 2015, 07:48:43 UTC
5c2923e Torsten Seemann 13 February 2015, 07:20:56 UTC Support .gbk/.embl files directly for --proteins trusted source 13 February 2015, 07:20:56 UTC
bb7e546 Torsten Seemann 13 February 2015, 06:47:04 UTC Replace hard coded 38 with already existing variable! 13 February 2015, 06:47:04 UTC
8ba6a96 Torsten Seemann 12 February 2015, 22:32:15 UTC Upgrade GNU Parallel 12 February 2015, 22:32:15 UTC
3b5c66a Torsten Seemann 12 February 2015, 22:31:38 UTC Tweak minced launcher script 12 February 2015, 22:31:38 UTC
f06d6de Torsten Seemann 13 November 2014, 03:14:05 UTC Add support for per CDS /transl_table codes 13 November 2014, 03:14:05 UTC
77f2e1c Torsten Seemann 26 August 2014, 01:35:33 UTC Fix Issue #34 where sig_peptide was still in AA not DNA coordinates! [Yevgeny Nikolaichik] 26 August 2014, 01:35:33 UTC
a8fffd6 Torsten Seemann 26 August 2014, 01:25:07 UTC Add TOC to documentation 26 August 2014, 01:25:07 UTC
ef9f993 Torsten Seemann 26 August 2014, 01:15:02 UTC Bump to version 1.11-dev 26 August 2014, 01:15:02 UTC
b379ffb Torsten Seemann 18 August 2014, 07:31:52 UTC New MACOSX binary for aragorn, prev one hung on some inputs 18 August 2014, 07:31:52 UTC
938acd0 Torsten Seemann 18 August 2014, 07:08:38 UTC Add --plain to GNU parallel to ignore global config (conflicts from ancient Ubuntu installs) 18 August 2014, 07:08:38 UTC
f067eed Torsten Seemann 08 August 2014, 05:03:22 UTC Ensure we don't include index files in tgz distribution 08 August 2014, 05:03:22 UTC
4910ff2 Torsten Seemann 28 July 2014, 07:49:12 UTC Bump to version 1.10 28 July 2014, 07:49:12 UTC
f92edc4 Torsten Seemann 28 July 2014, 07:34:26 UTC Tweaked locus_tag removal from /products to support 'c' suffix 28 July 2014, 07:34:26 UTC
2d078db Torsten Seemann 28 July 2014, 07:14:52 UTC Typo in help for --complaint // Inline citation 28 July 2014, 07:14:52 UTC
d904f04 Torsten Seemann 28 July 2014, 06:31:01 UTC Upgrade tbl2asn version to >= 23 as using new options plus old version 'expired' 28 July 2014, 06:31:01 UTC
75de007 Torsten Seemann 28 July 2014, 06:30:16 UTC Revert barrnap required version to 0.4 (as that supported 'arc') 28 July 2014, 06:30:16 UTC
a5c32c0 Torsten Seemann 28 July 2014, 06:10:29 UTC Remove path-extension msg() as it is done too early now 28 July 2014, 06:10:29 UTC
21a3ead Torsten Seemann 28 July 2014, 04:47:49 UTC Require latest barrnap with special archaea mode 28 July 2014, 04:47:49 UTC
4539a3e Torsten Seemann 28 July 2014, 04:46:00 UTC Print sequence ID when warning about length > 38 letters 28 July 2014, 04:46:00 UTC
8b436dc Torsten Seemann 28 July 2014, 04:42:54 UTC Disable low complexity filtering for BLASTP+ (-seg no) 28 July 2014, 04:42:54 UTC
91e60fd Torsten Seemann 28 July 2014, 04:36:53 UTC Latest command line options in docs 28 July 2014, 04:36:53 UTC
fcab33c Torsten Seemann 28 July 2014, 04:34:43 UTC Update citation in manual to non-epub 28 July 2014, 04:34:43 UTC
d6bc702 Torsten Seemann 28 July 2014, 04:32:20 UTC Merge branch 'master' of https://github.com/Victorian-Bioinformatics-Consortium/prokka 28 July 2014, 04:32:20 UTC
9d3ad0c Torsten Seemann 28 July 2014, 04:31:24 UTC Move TODO from docs to own file in git 28 July 2014, 04:31:24 UTC
7be5f85 Torsten Seemann 28 July 2014, 04:30:21 UTC Update and fix documentation 28 July 2014, 04:30:21 UTC
3a96509 Torsten Seemann 27 July 2014, 08:24:38 UTC Ignore genus files 27 July 2014, 08:24:38 UTC
77a5739 Torsten Seemann 27 July 2014, 08:20:13 UTC Issue #28 - Prokka now copes with --outdir with spaces in it! 27 July 2014, 08:20:13 UTC
73ab8d0 Torsten Seemann 27 July 2014, 01:04:00 UTC Added --rawproduct option to prevent cleaning of CDS product names 27 July 2014, 01:04:00 UTC
8971232 Torsten Seemann 27 July 2014, 00:55:16 UTC Add to wish list 27 July 2014, 00:55:16 UTC
924c36b Torsten Seemann 27 July 2014, 00:53:16 UTC Move "TO DO" list into its own file 27 July 2014, 00:53:16 UTC
d43b5c1 Torsten Seemann 27 July 2014, 00:30:13 UTC Ignore derived indices 27 July 2014, 00:30:13 UTC
f8f2d4b Torsten Seemann 27 July 2014, 00:27:09 UTC Instructions for installing without root privileges. 27 July 2014, 00:27:09 UTC
ead51ab Torsten Seemann 26 July 2014, 23:25:57 UTC Fix Issue #22 by replacing -file=>"cmd |" with "-|" and -fh=> 26 July 2014, 23:25:57 UTC
e4dfd70 Torsten Seemann 26 July 2014, 11:05:21 UTC Upgrade minced binary + min version to avoid bug in earlier version 26 July 2014, 11:05:21 UTC
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