| 460a152 | Torsten Seemann | 25 August 2016, 07:47:35 UTC | Update BLAST+ binaries to 2.4.0 | 25 August 2016, 07:47:35 UTC |
| 310a17f | Torsten Seemann | 25 August 2016, 05:49:57 UTC | Update tbl2asn binaries to version 25.0 | 25 August 2016, 05:49:57 UTC |
| 2f24e0b | Peter Cock | 15 August 2016, 09:52:26 UTC | EMBL validator now at v1.1.129 | 15 August 2016, 09:52:26 UTC |
| 04d59ae | Peter Cock | 10 August 2016, 14:00:26 UTC | EMBL validator moved (also now versioned) The EMBL flat file validator is now on GitHub, https://github.com/enasequence/sequencetools The JAR files are released on Maven Central, https://mvnrepository.com/artifact/uk.ac.ebi.ena.sequence/embl-api-validator See the recently updated home page, https://www.ebi.ac.uk/ena/software/flat-file-validator | 10 August 2016, 14:00:26 UTC |
| 4bf5747 | Torsten Seemann | 05 June 2016, 08:29:02 UTC | Disable /inference for --proteins and --hmms in --compliant mode (Issue #122) | 05 June 2016, 08:29:02 UTC |
| f61fd31 | Torsten Seemann | 04 June 2016, 02:31:39 UTC | Add Digest::MD5 stuff to docs and cleanup | 04 June 2016, 02:31:39 UTC |
| 6e864a6 | Torsten Seemann | 04 June 2016, 02:23:23 UTC | Merge pull request #148 from peterjc/patch-1 Outline of ENA submission from Prokka | 04 June 2016, 02:23:23 UTC |
| 42cebd6 | Torsten Seemann | 04 June 2016, 02:07:56 UTC | Upgrade prodigal binaries to 2.6.3 (Issue #166) | 04 June 2016, 02:07:56 UTC |
| b59adf4 | Torsten Seemann | 04 June 2016, 01:58:59 UTC | Skip signalp if >10,000 seqs (Issue #158) | 04 June 2016, 01:58:59 UTC |
| b0af252 | Torsten Seemann | 04 June 2016, 01:25:05 UTC | Use Digest::MD5 to ensure mac/linux compatibility re: md5sum (Issue #167) | 04 June 2016, 01:25:05 UTC |
| 92940bc | Torsten Seemann | 02 June 2016, 10:25:08 UTC | Reduce space used in contig ID in compliant mode | 02 June 2016, 10:25:08 UTC |
| dbf9c74 | Torsten Seemann | 02 June 2016, 10:04:49 UTC | Replace illegal | with _ in sequence IDs (Issue #155) | 02 June 2016, 10:05:12 UTC |
| 33ad502 | Torsten Seemann | 02 June 2016, 09:54:58 UTC | Add a conventional message of success (Issue #144) | 02 June 2016, 09:54:58 UTC |
| 3f2f185 | Torsten Seemann | 02 June 2016, 09:50:10 UTC | Autogenerate unique locus tag based on contigs MD5 (Issue #156) | 02 June 2016, 09:50:10 UTC |
| 2b38701 | Torsten Seemann | 02 June 2016, 09:07:30 UTC | Ensure bundled PATH exists before --setupdb called (Issue #160) | 02 June 2016, 09:07:30 UTC |
| 527c0c1 | Torsten Seemann | 02 June 2016, 08:59:48 UTC | Update kingdom BLAST databases to Uniprot May 2016 | 02 June 2016, 08:59:48 UTC |
| 325384b | Torsten Seemann | 02 June 2016, 08:59:07 UTC | Add -hash_index to makeblastdb (unsure if it helps) | 02 June 2016, 08:59:07 UTC |
| 059a793 | Torsten Seemann | 02 June 2016, 03:33:22 UTC | Use Java 1.6 instead of 1.8 for minced.jar bundled (Issue #162) | 02 June 2016, 03:33:22 UTC |
| 5bd0be1 | peterjc | 11 May 2016, 13:18:09 UTC | ENA will want your EMBL flat file gzipped. You will also likely need the MD5 checksum (certainly you will if you use FTP to upload the assembly.embl.gz file). | 11 May 2016, 13:18:09 UTC |
| 550e670 | Peter Cock | 17 December 2015, 11:06:48 UTC | Outline of ENA submission from Prokka Based on the discussion on #145 (Rebased Feb 2016 to use bash markup, and added some whitespace cleaup) | 11 May 2016, 13:14:40 UTC |
| 4abb143 | Torsten Seemann | 11 March 2016, 11:18:34 UTC | Update expired tbl2asn binaries from 24.3 to 24.9 | 11 March 2016, 11:18:34 UTC |
| 44a6576 | Torsten Seemann | 21 February 2016, 01:21:00 UTC | Update tbl2asn to http instead of ftp | 21 February 2016, 01:21:00 UTC |
| 5c20ec6 | Torsten Seemann | 21 February 2016, 01:18:29 UTC | Major update to installation instructions | 21 February 2016, 01:18:29 UTC |
| 2eb538d | Torsten Seemann | 29 November 2015, 06:59:23 UTC | Issue #87 : option --cdsrnaolap to allow tRNA/rRNA overlapping CDS | 29 November 2015, 06:59:23 UTC |
| 56bc27a | Torsten Seemann | 29 November 2015, 06:48:22 UTC | Issue #133 : sig_pep crud ends up in .FFN file | 29 November 2015, 06:48:22 UTC |
| 3fde5ca | Torsten Seemann | 29 November 2015, 06:27:35 UTC | Correctly check for bundled binaries in the 3 locations | 29 November 2015, 06:27:35 UTC |
| 168fa9e | Torsten Seemann | 29 November 2015, 06:09:04 UTC | Update HAMAP.hmm database | 29 November 2015, 06:09:04 UTC |
| b7bbf35 | Torsten Seemann | 29 November 2015, 05:29:37 UTC | Update core BLAST databases to Uniprot Nov-2015 | 29 November 2015, 05:29:37 UTC |
| 259b423 | Torsten Seemann | 28 November 2015, 07:40:35 UTC | Issue #116 : upgrade minced to avoid infinite loop in poly-N | 28 November 2015, 07:40:35 UTC |
| 678801c | Torsten Seemann | 28 November 2015, 07:36:13 UTC | Resolve Issue #110 : option --addmrna to add mRNA features for each CDS | 28 November 2015, 07:36:13 UTC |
| 6be2d8c | Torsten Seemann | 28 November 2015, 07:04:50 UTC | Issue #129 - set phase to empty for non-CDS features | 28 November 2015, 07:04:50 UTC |
| 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 |
