66a20cb | Jonathan Badger | 03 April 2015, 14:00:24 UTC | first version that can use refseq | 03 April 2015, 14:00:24 UTC |
1925896 | Jonathan Badger | 13 March 2015, 23:45:33 UTC | removed extra ZFILE from jsonQuery | 13 March 2015, 23:45:33 UTC |
828e640 | Jonathan Badger | 13 January 2015, 20:38:11 UTC | removed reannotation (not working) | 13 January 2015, 20:38:11 UTC |
1567d61 | Jonathan Badger | 26 November 2014, 18:47:22 UTC | allow saving alignments to be optional | 26 November 2014, 18:47:22 UTC |
32f0b7c | Jonathan Badger | 26 November 2014, 18:30:14 UTC | fix cases with peptide names with slashes | 26 November 2014, 18:30:14 UTC |
bba335c | Jonathan Badger | 13 November 2014, 19:07:00 UTC | output name is up to .json | 13 November 2014, 19:07:00 UTC |
bcf974b | Jonathan Badger | 13 November 2014, 18:45:12 UTC | utility script to breakup json file into pieces | 13 November 2014, 18:45:12 UTC |
83d4bcc | Jonathan Badger | 13 November 2014, 18:22:49 UTC | only print taxon_id if one assigned | 13 November 2014, 18:22:49 UTC |
3ee0dbc | Jonathan Badger | 13 November 2014, 00:13:36 UTC | ignore first level of classification if empty | 13 November 2014, 00:13:36 UTC |
1e6f9a4 | Jonathan Badger | 12 November 2014, 22:03:13 UTC | more less specific in reclassifyApis | 12 November 2014, 22:03:13 UTC |
19fc2ab | Jonathan Badger | 12 November 2014, 20:16:14 UTC | classify higher node if taxonomy of current node not found | 12 November 2014, 20:16:14 UTC |
7364c13 | Jonathan Badger | 05 November 2014, 20:06:11 UTC | reclassifyAPIS | 05 November 2014, 20:06:11 UTC |
8af1325 | Jonathan Badger | 19 March 2014, 19:15:45 UTC | Unclassfied category | 19 March 2014, 19:15:45 UTC |
bda785a | Jonathan Badger | 19 March 2014, 17:45:00 UTC | Merge branch 'master' of https://github.com/jhbadger/APIS | 19 March 2014, 17:45:00 UTC |
13776ce | Jonathan Badger | 19 March 2014, 17:44:39 UTC | zeroes in excel spreadsheet | 19 March 2014, 17:44:39 UTC |
24d130e | Jonathan Badger | 12 March 2014, 19:52:51 UTC | apisPie update Merge branch 'master' of jbadger2-osx:Projects/APIS | 12 March 2014, 19:52:51 UTC |
a5d9b82 | Jonathan Badger | 12 March 2014, 19:45:49 UTC | skip taxa with no taxonomy | 12 March 2014, 19:45:49 UTC |
c84e9a8 | Jonathan Badger | 05 March 2014, 01:12:21 UTC | Merge branch 'master' of https://github.com/jhbadger/APIS | 05 March 2014, 01:12:21 UTC |
dd7c29c | Jonathan Badger | 05 March 2014, 01:12:02 UTC | excel in apisPie | 05 March 2014, 01:12:02 UTC |
5e05ae3 | Jonathan Badger | 04 March 2014, 02:04:11 UTC | Merge branch 'master' of https://github.com/jhbadger/APIS | 04 March 2014, 02:04:11 UTC |
47f0578 | Jonathan Badger | 04 March 2014, 02:03:59 UTC | fix . in dataset | 04 March 2014, 02:03:59 UTC |
9a8e2ca | Jonathan Badger | 04 March 2014, 01:58:22 UTC | fix . in dataset | 04 March 2014, 01:58:22 UTC |
278da3a | Jonathan Badger | 03 March 2014, 07:55:08 UTC | apisPie | 03 March 2014, 07:55:08 UTC |
61fb085 | Jonathan Badger | 02 March 2014, 22:55:36 UTC | handle Ion Torrent Reads | 02 March 2014, 22:55:36 UTC |
a01e6b7 | Jonathan Badger | 31 January 2014, 19:26:10 UTC | working new grid system | 31 January 2014, 19:26:10 UTC |
825e892 | Jonathan Badger | 31 January 2014, 19:18:27 UTC | New Grid system | 31 January 2014, 19:18:27 UTC |
a9db6d6 | Jonathan Badger | 30 December 2013, 17:39:30 UTC | allowed split datanases in apisTimeLogicBlast | 30 December 2013, 17:39:30 UTC |
496dc92 | Jonathan Badger | 27 December 2013, 16:59:53 UTC | fixed array issue for apisTimeLogicBlast | 27 December 2013, 16:59:53 UTC |
3d051fe | Jonathan Badger | 19 December 2013, 23:52:22 UTC | Grid APIS now working again | 19 December 2013, 23:52:22 UTC |
3dc748d | Jonathan Badger | 19 December 2013, 22:57:22 UTC | goxed fastacmd error | 19 December 2013, 22:57:22 UTC |
08cb68b | Jonathan Badger | 19 December 2013, 22:33:21 UTC | don't report errors in fastacmd | 19 December 2013, 22:33:21 UTC |
919a2d4 | Jonathan Badger | 19 December 2013, 22:28:34 UTC | handle multiple taxonomies and databases | 19 December 2013, 22:28:34 UTC |
a2e5789 | Jonathan Badger | 12 December 2013, 22:37:49 UTC | new source base | 12 December 2013, 22:37:49 UTC |
7d5f8ad | Jonathan Badger | 10 January 2013, 19:39:02 UTC | fastercsv rather than csb for 1.8 | 10 January 2013, 19:39:02 UTC |
be4b986 | Jonathan Badger | 08 January 2013, 21:30:48 UTC | use fastercsv in findTrees | 08 January 2013, 21:30:48 UTC |
5a10ba2 | Jonathan Badger | 08 January 2013, 21:29:07 UTC | use fastcsv in findTrees | 08 January 2013, 21:29:07 UTC |
9817719 | Jonathan Badger | 20 December 2012, 23:36:34 UTC | removed 1.9.2 requirement | 20 December 2012, 23:36:34 UTC |
4b96d77 | Jonathan Badger | 14 September 2012, 17:06:30 UTC | Allow phylometarep format | 14 September 2012, 17:06:30 UTC |
15649ea | Jonathan Badger | 13 September 2012, 18:58:26 UTC | have separate uniq step in mrerge blast to remove redundant lines | 13 September 2012, 18:58:26 UTC |
dd6f9b7 | Jonathan Badger | 13 September 2012, 17:57:41 UTC | Changes to work with multi-blast from phylometarep | 13 September 2012, 17:57:41 UTC |
5a96fc2 | Jonathan Badger | 15 August 2012, 19:44:52 UTC | allow null uri | 15 August 2012, 19:44:52 UTC |
55ae7f7 | Jonathan Badger | 15 August 2012, 19:41:26 UTC | mods for phylodb 1.05 | 15 August 2012, 19:41:26 UTC |
a9587e8 | Jonathan Badger | 31 July 2012, 21:03:56 UTC | mysql server gone away better handling | 31 July 2012, 21:03:56 UTC |
1a80afa | Jonathan Badger | 03 July 2012, 20:01:31 UTC | check to see if support progs exist | 03 July 2012, 20:01:31 UTC |
f0d5173 | Jonathan Badger | 03 July 2012, 17:03:10 UTC | check for apis version | 03 July 2012, 17:03:10 UTC |
2221328 | Jonathan Badger | 09 May 2012, 17:05:55 UTC | Linux version of support bin | 09 May 2012, 17:05:55 UTC |
0bdee28 | Jonathan Badger | 08 May 2012, 22:58:30 UTC | remove dependency on environmental variables for paths | 08 May 2012, 22:58:30 UTC |
4e29d11 | Jonathan Badger | 20 March 2012, 16:48:27 UTC | normal metarep, not phylo-metarep | 20 March 2012, 16:48:27 UTC |
e06ae34 | Jonathan Badger | 20 March 2012, 16:01:45 UTC | metaLink or ncbi link as needed | 20 March 2012, 16:01:45 UTC |
31b7a2e | Jonathan Badger | 20 March 2012, 15:48:39 UTC | metaLink link to metarep | 20 March 2012, 15:48:39 UTC |
656cf38 | Jonathan Badger | 23 February 2012, 23:46:55 UTC | add close at start of apisRun to free connection | 23 February 2012, 23:46:55 UTC |
7f86621 | Jonathan Badger | 23 February 2012, 22:46:59 UTC | fixed empty homolog file problem | 23 February 2012, 22:46:59 UTC |
45dc352 | Jonathan Badger | 23 February 2012, 21:25:05 UTC | =, not == in sql | 23 February 2012, 21:25:05 UTC |
fd896f6 | Jonathan Badger | 23 February 2012, 21:18:44 UTC | have unprocessed flag | 23 February 2012, 21:18:44 UTC |
2fa8736 | Jonathan Badger | 23 February 2012, 21:06:20 UTC | close database connection after every query to hopefully improve grid performance | 23 February 2012, 21:06:20 UTC |
bc4f69f | Jonathan Badger | 23 February 2012, 19:26:55 UTC | added separate time logic blast script | 23 February 2012, 19:26:55 UTC |
a7fe870 | Jonathan Badger | 15 February 2012, 01:00:30 UTC | added rescue for root node bootstrap | 15 February 2012, 01:00:30 UTC |
b6595db | Jonathan Badger | 07 February 2012, 01:19:38 UTC | handle empty alignment | 07 February 2012, 01:19:38 UTC |
cb5c01b | Jonathan Badger | 04 February 2012, 02:33:21 UTC | skipTree option | 04 February 2012, 02:33:21 UTC |
eb16573 | Jonathan Badger | 03 February 2012, 18:42:43 UTC | removed redundant scripts | 03 February 2012, 18:42:43 UTC |
101c6c0 | Jonathan Badger | 03 February 2012, 18:42:11 UTC | supplementary scripts now working | 03 February 2012, 18:42:11 UTC |
5be4eac | Jonathan Badger | 03 February 2012, 18:03:09 UTC | fixed wrong # of args in createClassification | 03 February 2012, 18:03:09 UTC |
fa8fae4 | Jonathan Badger | 03 February 2012, 00:33:27 UTC | createApisCSV works | 03 February 2012, 00:33:27 UTC |
fc883a7 | Jonathan Badger | 01 February 2012, 19:28:46 UTC | timelogic database find | 01 February 2012, 19:28:46 UTC |
f65da22 | Jonathan Badger | 01 February 2012, 16:55:06 UTC | restore rescue to processTree | 01 February 2012, 16:55:06 UTC |
433c274 | Jonathan Badger | 01 February 2012, 16:31:30 UTC | use proteindb name for timelogic | 01 February 2012, 16:31:30 UTC |
ff9f351 | Jonathan Badger | 01 February 2012, 16:23:01 UTC | fixed tax string in ApisDB | 01 February 2012, 16:23:01 UTC |
f456057 | Jonathan Badger | 31 January 2012, 23:41:41 UTC | APIS using phylodb 1.04 first version | 31 January 2012, 23:41:41 UTC |
1979ff5 | Jonathan Badger | 14 October 2011, 23:32:34 UTC | propagate database option to grid jobs | 14 October 2011, 23:32:34 UTC |
419be3b | Jonathan Badger | 14 October 2011, 22:47:47 UTC | allow choice of protein database in APIS | 14 October 2011, 22:47:47 UTC |
317b0fc | Jonathan Badger | 14 October 2011, 20:47:53 UTC | option to avoid recreating existing reports in createApisCSV | 14 October 2011, 20:47:53 UTC |
581c2dc | Jonathan Badger | 12 October 2011, 20:38:34 UTC | remove duplicates | 12 October 2011, 20:38:34 UTC |
4650c0f | Jonathan Badger | 12 October 2011, 18:37:43 UTC | improved blast query for top hit | 12 October 2011, 18:37:43 UTC |
e4ac75c | Jonathan Badger | 11 October 2011, 22:42:45 UTC | remove redundant header | 11 October 2011, 22:42:45 UTC |
0dd8814 | Jonathan Badger | 11 October 2011, 22:40:35 UTC | more efficient blast full in createApisCSV | 11 October 2011, 22:40:35 UTC |
0dc247c | Jonathan Badger | 10 October 2011, 19:37:26 UTC | add identity, coverage to blast report in createApisCSV | 10 October 2011, 19:37:26 UTC |
558afd7 | Jonathan Badger | 09 October 2011, 14:42:03 UTC | fix colons screwing up trees | 09 October 2011, 14:42:03 UTC |
d83d638 | Jonathan Badger | 09 October 2011, 14:00:37 UTC | timelogic blast | 09 October 2011, 14:00:37 UTC |
de35b6b | Jonathan Badger | 08 October 2011, 01:06:41 UTC | improved configuration | 08 October 2011, 01:06:41 UTC |
ea71714 | Jonathan Badger | 07 October 2011, 22:46:04 UTC | configuration file of host | 07 October 2011, 22:46:04 UTC |
0a6233b | Jonathan Badger | 07 October 2011, 21:32:08 UTC | fixed insert issue | 07 October 2011, 21:32:08 UTC |
a77e8d5 | Jonathan Badger | 07 October 2011, 20:00:09 UTC | fix annotation | 07 October 2011, 20:00:09 UTC |
f1b1d36 | Jonathan Badger | 07 October 2011, 19:34:31 UTC | test version of new apis | 07 October 2011, 19:34:31 UTC |
86d250a | Jonathan Badger | 06 October 2011, 20:09:15 UTC | count method | 06 October 2011, 20:09:15 UTC |
147040b | Jonathan Badger | 06 October 2011, 20:02:40 UTC | WebAPIS | 06 October 2011, 20:02:40 UTC |
62e3938 | Jonathan Badger | 06 October 2011, 19:30:21 UTC | moved to sql for efficency | 06 October 2011, 19:30:21 UTC |
1498121 | Jonathan Badger | 04 October 2011, 19:55:41 UTC | moved favicon | 04 October 2011, 19:55:41 UTC |
382d504 | Jonathan Badger | 04 October 2011, 19:33:57 UTC | icon | 04 October 2011, 19:33:57 UTC |
18b6d71 | Jonathan Badger | 04 October 2011, 18:35:20 UTC | to_s before quite | 04 October 2011, 18:35:20 UTC |
9ab446d | Jonathan Badger | 04 October 2011, 16:06:39 UTC | quoting of single quotes | 04 October 2011, 16:06:39 UTC |
25f6f48 | Jonathan Badger | 03 October 2011, 20:54:39 UTC | fixed relaxed classification | 03 October 2011, 20:54:39 UTC |
f988e78 | Jonathan Badger | 22 September 2011, 23:53:59 UTC | allow taxonomies without spaces | 22 September 2011, 23:53:59 UTC |
8fc1ad4 | Jonathan Badger | 21 September 2011, 21:45:59 UTC | Merge branch 'master' of github.com:jhbadger/APIS | 21 September 2011, 21:45:59 UTC |
b168517 | Jonathan Badger | 21 September 2011, 21:45:13 UTC | active_record apisPie, createApisCSV | 21 September 2011, 21:45:13 UTC |
542fe43 | Jonathan Badger | 16 September 2011, 19:39:48 UTC | fixed parsing of RAST scaffolds | 16 September 2011, 19:39:48 UTC |
c22a7ca | Jonathan Badger | 30 August 2011, 22:20:23 UTC | only add database if not there already | 30 August 2011, 22:20:23 UTC |
66a316e | Jonathan Badger | 26 August 2011, 00:21:35 UTC | Active Record | 26 August 2011, 00:21:35 UTC |
2e8f7be | Jonathan Badger | 17 August 2011, 20:27:45 UTC | fixed typo | 17 August 2011, 20:27:45 UTC |
cedb1bb | Jonathan Badger | 17 August 2011, 19:32:14 UTC | remove apisRun, _input from dataset name on grid | 17 August 2011, 19:32:14 UTC |
67d3efe | Jonathan Badger | 17 August 2011, 17:49:20 UTC | don't have .pep on input files grid doesn't like it | 17 August 2011, 17:49:20 UTC |