| fc777c2 | Niels Hanson | 26 November 2015, 04:09:54 UTC | Added back GenBank file creation | 26 November 2015, 04:09:54 UTC |
| 9a34877 | Niels Hanson | 25 November 2015, 21:07:40 UTC | Merge branch 'master' of https://github.com/hallamlab/metapathways2 | 25 November 2015, 21:07:40 UTC |
| a7a826c | Niels Hanson | 25 November 2015, 21:07:24 UTC | Corrected RPKM buffer-overflow and memory leak problems, corrected argument parsing | 25 November 2015, 21:07:24 UTC |
| 5b9b9bf | Niels Hanson | 01 November 2015, 20:13:52 UTC | Added metapathways logo to README | 01 November 2015, 20:13:52 UTC |
| a601ce4 | Niels Hanson | 07 July 2015, 19:01:46 UTC | Update README with v2.5.2 information | 07 July 2015, 19:01:46 UTC |
| 5b278da | Niels Hanson | 07 July 2015, 18:54:23 UTC | v2.5.2 release | 07 July 2015, 18:54:23 UTC |
| 81100ea | Niels Hanson | 04 July 2015, 01:47:38 UTC | Fixed rRNA DB formatting problem, GenBank input file misses, rpkm calculation from .sam files | 04 July 2015, 01:47:38 UTC |
| 76bc587 | Niels Hanson | 03 July 2015, 21:27:36 UTC | Updated citation | 03 July 2015, 21:27:36 UTC |
| 05ac7c8 | Niels Hanson | 03 July 2015, 20:35:03 UTC | Updated gitignore | 03 July 2015, 20:35:03 UTC |
| bc2b329 | Niels Hanson | 08 May 2015, 23:48:31 UTC | Merge branch 'master' of https://github.com/hallamlab/metapathways2 | 08 May 2015, 23:48:31 UTC |
| 0dd223b | Niels Hanson | 08 May 2015, 23:48:02 UTC | Started unit tests for MP scripts | 08 May 2015, 23:48:02 UTC |
| 643826d | Niels Hanson | 09 March 2015, 19:59:02 UTC | Fixed bug preventing annotations from gbk files being used. | 09 March 2015, 19:59:02 UTC |
| 9185355 | kishori | 25 February 2015, 17:13:50 UTC | Merge branch 'master' of https://github.com/kishori82/metapathways2 | 25 February 2015, 17:13:50 UTC |
| 7697332 | kishori | 25 February 2015, 17:13:39 UTC | format LAST from 40M to 4000M ; parse blast optimized | 25 February 2015, 17:13:39 UTC |
| 9ae4d84 | Niels Hanson | 22 February 2015, 18:53:01 UTC | Updated frontpage with citation. | 22 February 2015, 18:53:01 UTC |
| 08a5b82 | nielshanson | 21 February 2015, 01:27:15 UTC | Updated lastal binary | 21 February 2015, 01:27:15 UTC |
| f5dd47e | Niels Hanson | 20 February 2015, 22:40:42 UTC | Made float comparisons more stable; confirmed new BSR computation on OSX | 20 February 2015, 22:40:42 UTC |
| e54c6da | kishori | 20 February 2015, 19:45:01 UTC | removed old lastal | 20 February 2015, 19:45:01 UTC |
| 5261480 | kishori | 20 February 2015, 19:41:11 UTC | Added remaining files for pull | 20 February 2015, 19:41:11 UTC |
| 6177e0a | kishori | 20 February 2015, 19:39:23 UTC | adeed formatdb | 20 February 2015, 19:39:23 UTC |
| fe4babe | kishori | 20 February 2015, 19:36:27 UTC | Fixed automatic picking up of param and config files, fixed refscore calculation to make independent of BLAST and LAST executables, adjust parse balst file to compute the bitscore internally from alignment refscores | 20 February 2015, 19:36:27 UTC |
| 50b5572 | nielshanson | 10 February 2015, 03:53:54 UTC | Updated stale lastdb and lastal binaries for Ubuntu | 10 February 2015, 03:53:54 UTC |
| 8b88514 | kishori | 05 February 2015, 03:07:56 UTC | Merge branch 'master' of https://github.com/kishori82/metapathways2 | 05 February 2015, 03:07:56 UTC |
| 140712c | kishori | 05 February 2015, 03:07:47 UTC | fixed BLAST autoformatting problem and collapsed annotation orfs, pathologic input and report generation | 05 February 2015, 03:07:47 UTC |
| 5e57517 | Niels Hanson | 13 January 2015, 00:29:05 UTC | added back all the executables | 13 January 2015, 00:29:05 UTC |
| ad4c5af | kishori | 07 January 2015, 19:53:54 UTC | Fixed reformatting of old databases, rpkm sam file issue | 07 January 2015, 19:53:54 UTC |
| 3e24c37 | kishori | 08 December 2014, 23:23:56 UTC | fixed empty file | 08 December 2014, 23:23:56 UTC |
| e39b96b | Kishori Mohan Konwar | 08 December 2014, 03:44:07 UTC | Added error for lastal failure | 08 December 2014, 03:44:07 UTC |
| 3d260ba | kishori | 08 December 2014, 02:21:54 UTC | Added the provision for invalid file | 08 December 2014, 02:21:54 UTC |
| 9a8d6b2 | kishori | 05 December 2014, 19:05:30 UTC | Merge branch 'master' of https://github.com/kishori82/metapathways2 | 05 December 2014, 19:05:30 UTC |
| bda5ac9 | kishori | 05 December 2014, 19:05:02 UTC | Fixed to skip samples with incorrect input | 05 December 2014, 19:05:02 UTC |
| dcd1cc3 | Niels Hanson | 27 November 2014, 18:13:01 UTC | Update README.md | 27 November 2014, 18:13:01 UTC |
| 9df0b6d | Niels Hanson | 27 November 2014, 17:44:50 UTC | Update README.md | 27 November 2014, 17:44:50 UTC |
| ed24df9 | Niels Hanson | 27 November 2014, 17:44:37 UTC | Updated with links to the new v2.5 release. | 27 November 2014, 17:44:37 UTC |
| 9521205 | Niels Hanson | 27 November 2014, 17:23:00 UTC | Updated readme | 27 November 2014, 17:23:00 UTC |
| 0bbbb57 | nielshanson | 27 November 2014, 04:50:26 UTC | Merge branch 'master' of https://github.com/hallamlab/metapathways2 | 27 November 2014, 04:50:26 UTC |
| ecd9037 | nielshanson | 27 November 2014, 04:49:31 UTC | Updated Ubuntu executables and small fix to jobscreator.py NCBI_TAXONOMY_TREE.txt to ncbi_taxonomy_tree.txt | 27 November 2014, 04:49:31 UTC |
| 25586a5 | kishori | 27 November 2014, 04:37:59 UTC | removed some stray files | 27 November 2014, 04:37:59 UTC |
| 216a4d8 | kishori | 27 November 2014, 04:08:00 UTC | minor fix | 27 November 2014, 04:08:00 UTC |
| 9566647 | kishori | 26 November 2014, 02:37:43 UTC | Deleted MetaPathways2 | 26 November 2014, 02:37:43 UTC |
| c5d9503 | kishori | 26 November 2014, 02:34:57 UTC | Added a Ubuntu binary | 26 November 2014, 02:34:57 UTC |
| fbfdd8e | kishori | 24 November 2014, 23:45:56 UTC | Added regtests, upto date binaries, removed MLTreeMap data, after a pull | 24 November 2014, 23:45:56 UTC |
| e6c3489 | kishori | 24 November 2014, 23:43:49 UTC | Merge branch 'master' of https://github.com/kishori82/metapathways2 | 24 November 2014, 23:43:49 UTC |
| 36473e5 | kishori | 24 November 2014, 23:43:25 UTC | Added regtests, upto date binaries, removed MLTreeMap data | 24 November 2014, 23:43:25 UTC |
| 09cb0f8 | Niels Hanson | 18 November 2014, 00:54:27 UTC | Prevent removal of 'hypothetical protein' annotations in annotate_fast.py | 18 November 2014, 00:54:27 UTC |
| b37e579 | Niels Hanson | 18 November 2014, 00:09:45 UTC | Updated create_reports_fast.py to print the full ORF annotation to functional_and_taxonomic_table.txt with the original taxonomy. | 18 November 2014, 00:09:45 UTC |
| c13e405 | kishori | 05 November 2014, 20:26:25 UTC | Fixed the file type detection | 05 November 2014, 20:26:25 UTC |
| 1f8a83f | Niels Hanson | 24 October 2014, 23:15:22 UTC | Added MetaPatwhays2 GUI executable | 24 October 2014, 23:15:22 UTC |
| b237cda | Niels Hanson | 24 October 2014, 20:55:41 UTC | Added Ubunutu-compatible GUI and binaries | 24 October 2014, 20:55:41 UTC |
| 7512f14 | Niels Hanson | 15 October 2014, 22:23:09 UTC | added back executables | 15 October 2014, 22:23:09 UTC |
| 5047e7d | Niels Hanson | 15 October 2014, 21:41:18 UTC | Updated MetaPathways_DBs.zip with support files Updated CAZy and NCBI Taxonomy Database support files for WTD. | 15 October 2014, 21:41:18 UTC |
| 22559e5 | kishori | 15 October 2014, 21:00:40 UTC | changed in PNNL | 15 October 2014, 21:00:40 UTC |
| d279920 | kishori | 04 October 2014, 03:28:48 UTC | Merge branch 'master' of https://github.com/kishori82/metapathways2 Conflicts: config/template_config.txt config/template_param.txt | 04 October 2014, 03:28:48 UTC |
| 44f3337 | kishori | 03 October 2014, 20:31:13 UTC | NO changes in particular | 03 October 2014, 20:31:13 UTC |
| 17eff2c | Niels Hanson | 03 October 2014, 03:48:28 UTC | No need for test file | 03 October 2014, 03:48:28 UTC |
| d4bf8e8 | Niels Hanson | 03 October 2014, 03:43:56 UTC | Merge branch 'master' of https://github.com/hallamlab/metapathways2 Updated changes made of mayas machine. | 03 October 2014, 03:43:56 UTC |
| 0e29ab4 | Niels Hanson | 03 October 2014, 03:43:30 UTC | testing github | 03 October 2014, 03:43:30 UTC |
| 8184912 | Niels Hanson | 03 October 2014, 03:40:04 UTC | Tested run_pathologic.py on Maya's samples | 03 October 2014, 03:40:04 UTC |
| 61aa62f | Niels Hanson | 03 October 2014, 03:38:40 UTC | Updated wtih printf changes | 03 October 2014, 03:38:40 UTC |
| 851ed1b | Niels Hanson | 03 October 2014, 00:33:29 UTC | Updated run pathologic | 03 October 2014, 00:33:29 UTC |
| f324f2f | Niels Hanson | 30 September 2014, 00:17:00 UTC | Added metapathways .dmg file | 30 September 2014, 00:17:00 UTC |
| c83e237 | Niels Hanson | 28 September 2014, 03:07:11 UTC | Fixed some bugs in the WTD code. WTD calculation is now more robust. Preferred taxa from MEGAN's mapping file is integrated into reports from the ncbi.map file. | 28 September 2014, 03:07:11 UTC |
| dfb3f3d | Niels Hanson | 24 September 2014, 22:36:20 UTC | Merge remote-tracking branch 'origin/master' Conflicts: libs/python_scripts/MetaPathways_annotate_fast.py | 24 September 2014, 22:36:20 UTC |
| b933d64 | Niels Hanson | 24 September 2014, 22:35:06 UTC | Integrated WTD into MetaPathways_run_pathologic.py and runs with the standard jobscreator.py script | 24 September 2014, 22:35:06 UTC |
| d900f0b | kishori | 24 September 2014, 18:57:37 UTC | MetaPathways 2.5 | 24 September 2014, 18:57:37 UTC |
| 9ddb35b | kishori | 20 September 2014, 03:31:24 UTC | Fixed cazy | 20 September 2014, 03:31:24 UTC |
| 74efc06 | kishori | 20 September 2014, 03:30:23 UTC | Merge branch 'master' of https://github.com/kishori82/metapathways2 | 20 September 2014, 03:30:23 UTC |
| 6872562 | kishori | 20 September 2014, 03:29:50 UTC | Fixed cazy | 20 September 2014, 03:29:50 UTC |
| e1c0fa6 | Niels Hanson | 18 September 2014, 01:36:26 UTC | Updated WTD code in MetaPathways_pathway_table.py. Computes and outputs WTD correctly. Just needs to be integrated. | 18 September 2014, 01:36:26 UTC |
| a54aa01 | Niels Hanson | 17 September 2014, 04:01:30 UTC | Updated WTD code. Still need to format results and integrate with main pipeline code. | 17 September 2014, 04:01:30 UTC |
| 80bffb5 | kishori | 16 September 2014, 21:48:50 UTC | Changed after the RPKM changes | 16 September 2014, 21:48:50 UTC |
| 3c5eb57 | Kishori | 15 September 2014, 19:07:26 UTC | Added RPKM code. | 15 September 2014, 19:07:26 UTC |
| b5b2deb | nielshanson | 12 September 2014, 22:53:23 UTC | Updated some of the config files. Texting PyCharm development environment. | 12 September 2014, 22:53:23 UTC |
| a4d93e0 | nielshanson | 04 September 2014, 04:59:23 UTC | spelling | 04 September 2014, 04:59:23 UTC |
| f68123b | Niels Hanson | 04 September 2014, 04:58:12 UTC | Updated readme with db link | 04 September 2014, 04:58:12 UTC |
| c6952db | Niels Hanson | 04 September 2014, 04:52:35 UTC | updated with Unix MP GUI executable | 04 September 2014, 04:52:35 UTC |
| aebfcf2 | Niels Hanson | 19 August 2014, 19:54:12 UTC | openSUSE binaries | 19 August 2014, 19:54:12 UTC |
| 5d08e71 | Niels Hanson | 19 August 2014, 19:03:43 UTC | updated unix binaries | 19 August 2014, 19:03:43 UTC |
| 6f488c9 | Niels Hanson | 19 August 2014, 00:12:37 UTC | addressed missing sequences failing parse issue #12 | 19 August 2014, 00:12:37 UTC |
| 02642ea | Niels Hanson | 18 August 2014, 23:13:31 UTC | modifed rpkm and wise binaries for easier compilation on 64-bit unix | 18 August 2014, 23:13:31 UTC |
| 8d7f089 | Niels Hanson | 16 August 2014, 00:09:35 UTC | Updated functions with comments and fixed a small bug formatting rRNA sequences | 16 August 2014, 00:09:35 UTC |
| 35ae708 | Niels Hanson | 13 August 2014, 22:32:07 UTC | Updated readme instructions | 13 August 2014, 22:32:07 UTC |
| 07e9834 | Niels Hanson | 13 August 2014, 22:24:47 UTC | Added the Mac .dmg file | 13 August 2014, 22:24:47 UTC |
| 7bf3eb3 | Kishori Mohan Konwar | 12 August 2014, 14:58:23 UTC | Added the MetaPathways_func_search and MetaPathways_tRNA_scan | 12 August 2014, 14:58:23 UTC |
| 9e2d4aa | Kishori Mohan Konwar | 10 August 2014, 18:06:48 UTC | add last to the repository | 10 August 2014, 18:06:48 UTC |
| fdf2e08 | Kishori Mohan Konwar | 10 August 2014, 17:54:41 UTC | Adding the executables | 10 August 2014, 17:54:41 UTC |
| 22bfbbf | Kishori Mohan Konwar | 10 August 2014, 17:52:56 UTC | Chaning the executabales | 10 August 2014, 17:52:56 UTC |
| 5ff2bcc | Kishori Konwar | 10 August 2014, 17:01:29 UTC | added the config and param files | 10 August 2014, 17:01:29 UTC |
| 640b16f | Kishori Konwar | 10 August 2014, 16:07:18 UTC | Added the prodigal script | 10 August 2014, 16:07:18 UTC |
| b971e67 | Kishori Konwar | 10 August 2014, 00:00:25 UTC | removed the separate MLTreeCode | 10 August 2014, 00:00:25 UTC |
| ddb80c7 | Kishori Konwar | 05 August 2014, 06:58:05 UTC | Added the MLTReemap | 05 August 2014, 06:58:05 UTC |
| 33e820d | Kishori Konwar | 25 July 2014, 05:56:59 UTC | Made changes to add automatic pathway tools start and stop | 25 July 2014, 05:56:59 UTC |
| 0cd1cbd | Kishori Konwar | 15 July 2014, 20:04:00 UTC | Fixed the Build pgdb issue | 15 July 2014, 20:04:00 UTC |
| 6fcfc5a | Kishori Konwar | 07 July 2014, 18:38:56 UTC | Merge branch 'master' of https://github.com/kishori82/metapathways2 "removed some legacy code" | 07 July 2014, 18:38:56 UTC |
| 025e455 | Kishori Konwar | 07 July 2014, 18:37:03 UTC | Removed some legacy code and fixed to run multiplse samples bug | 07 July 2014, 18:37:03 UTC |
| 53f8020 | Niels Hanson | 05 July 2014, 05:17:21 UTC | Fixed formatdb path in diagnoze.py | 05 July 2014, 05:17:21 UTC |
| dbc6a0e | Kishori Konwar | 05 July 2014, 01:22:54 UTC | Fixed the parse blast to check the loggers are not NoneType | 05 July 2014, 01:22:54 UTC |
| 96fffbf | Kishori Konwar | 02 July 2014, 01:03:15 UTC | Fixed code to deal with the selective overwrite | 02 July 2014, 01:03:15 UTC |
| ccf1728 | Kishori Konwar | 01 July 2014, 00:32:09 UTC | added the gbk-annotate and gbk-unannotate | 01 July 2014, 00:32:09 UTC |
| 66aaf2d | Kishori Konwar | 28 June 2014, 21:02:47 UTC | Some minor changes | 28 June 2014, 21:02:47 UTC |
