Skip to main content

Browse the archive

https://github.com/jorvis/ergatis
06 April 2024, 03:28:40 UTC
sort by:
Revision Author Date Message Commit Date
124aafc Shaun Adkins 04 January 2023, 15:16:46 UTC fixed perl path 04 January 2023, 15:16:46 UTC
40e7483 Shaun Adkins 07 December 2022, 13:50:21 UTC fixing bad tar command 07 December 2022, 13:50:21 UTC
632b42c Shaun Adkins 14 September 2021, 19:41:31 UTC one more fix related to previous commit 14 September 2021, 19:41:31 UTC
7e3a837 Shaun Adkins 14 September 2021, 19:38:35 UTC preventing c-based components from compiling due to rhel8 issues 14 September 2021, 19:38:35 UTC
c864d55 Shaun Adkins 14 September 2021, 19:29:46 UTC commenting out building of src code using c 14 September 2021, 19:29:46 UTC
de70a94 Shaun Adkins 14 September 2021, 15:11:36 UTC adding debug option to lipop component to not redirect STDERR to /dev/null 14 September 2021, 15:11:36 UTC
e722d92 Shaun Adkins 14 September 2021, 14:49:07 UTC adding STDERR param to lipop component 14 September 2021, 14:49:07 UTC
213c81c Shaun Adkins 28 July 2021, 19:16:52 UTC fixing a typo in the config 28 July 2021, 19:16:52 UTC
2c1d773 Shaun Adkins 28 July 2021, 19:13:20 UTC fixing a typo in the config 28 July 2021, 19:13:20 UTC
28bc757 Shaun Adkins 16 June 2021, 19:15:06 UTC adding dceSpecChanger script which is used in run_pipeline.cgi 16 June 2021, 19:15:06 UTC
fea2efb Shaun Adkins 14 June 2021, 14:28:59 UTC Merge branch 'master' of https://github.com/jorvis/ergatis 14 June 2021, 14:28:59 UTC
00c3577 Shaun Adkins 14 June 2021, 14:28:38 UTC changing path 14 June 2021, 14:28:38 UTC
a0d125a Shaun Adkins 18 February 2021, 20:09:10 UTC fixing blastp 18 February 2021, 20:09:10 UTC
49ddcfc Shaun Adkins 18 February 2021, 19:41:37 UTC updating blast-plus components to match lgtseek ones 18 February 2021, 19:41:37 UTC
f46a35b Shaun Adkins 15 January 2021, 14:28:20 UTC updated htdocs for RHEL8 compatibility 15 January 2021, 14:28:20 UTC
102b913 Shaun Adkins 28 October 2020, 17:23:18 UTC changing to alternative POST call implementation 28 October 2020, 17:23:18 UTC
842bc78 Shaun Adkins 29 September 2020, 15:19:27 UTC removing eggNOG from annotation hierarchy 29 September 2020, 15:19:27 UTC
1dee8ae Shaun Adkins 24 September 2020, 18:41:39 UTC added some ambiguous terms to eggnog and ber parsers 24 September 2020, 18:41:39 UTC
b77bc02 Shaun Adkins 28 August 2020, 18:15:30 UTC scp_files component staging area is now more configurable 28 August 2020, 18:15:30 UTC
f96d1d9 Shaun Adkins 27 August 2020, 18:18:06 UTC removing config names from header mappings 27 August 2020, 18:18:06 UTC
6e6bd5c Shaun Adkins 19 August 2020, 19:58:10 UTC map_headers_to_tab now accounts for multiple contigs 19 August 2020, 19:58:10 UTC
1081ede Shaun Adkins 12 July 2019, 19:46:50 UTC fixing potential bug with sqlite3 search 12 July 2019, 19:46:50 UTC
05c0559 Shaun Adkins 12 July 2019, 19:27:43 UTC added cases for non-Uniref hits 12 July 2019, 19:27:43 UTC
964ceb3 Shaun Adkins 24 May 2019, 13:28:25 UTC fixing configuration 24 May 2019, 13:28:25 UTC
0852f42 Shaun Adkins 23 May 2019, 15:36:23 UTC sourcing some python3 envvars for internal use 23 May 2019, 15:36:23 UTC
f93682e Shaun Adkins 23 May 2019, 15:08:22 UTC fixing bug 23 May 2019, 15:08:22 UTC
b8e43a5 Shaun Adkins 28 March 2019, 19:05:01 UTC adding ability to call dceSpecChanger.pl after a rerun command 28 March 2019, 19:05:01 UTC
3ac4b0c Shaun Adkins 14 March 2019, 14:08:10 UTC removing quotes from prodical config 14 March 2019, 14:08:10 UTC
8c24576 Shaun Adkins 08 March 2019, 18:15:24 UTC fixing incorrect mapping file name 08 March 2019, 18:15:24 UTC
e33f178 Shaun Adkins 26 February 2019, 13:37:59 UTC changed prodigal command opts 26 February 2019, 13:37:59 UTC
fe78cc0 Shaun Adkins 04 February 2019, 15:50:01 UTC attempting to fix issue with incorrect manatee sequence dump in genecalls pipeline 04 February 2019, 15:50:01 UTC
294f25e Shaun Adkins 31 January 2019, 18:22:09 UTC modified pipeline_summary to use correct bsml2fasta output 31 January 2019, 18:22:09 UTC
72b853a Shaun Adkins 13 December 2018, 15:57:36 UTC fixing bug where glimmer output was on wrong strand 13 December 2018, 15:57:36 UTC
fd961a2 Shaun Adkins 11 December 2018, 15:32:13 UTC fixed issue with genecalls layout for chado not being used 11 December 2018, 15:32:13 UTC
7c3d944 Shaun Adkins 10 December 2018, 19:45:27 UTC temporary hardcoding of chado_record_uniq to production version until we can figure outgcc bug 10 December 2018, 19:45:27 UTC
1d1e0b9 Shaun Adkins 10 December 2018, 18:49:55 UTC take 4 on fixing chado_record_uniq 10 December 2018, 18:49:55 UTC
2e525b4 Shaun Adkins 10 December 2018, 18:34:46 UTC take 4 on fixing chado_record_uniq 10 December 2018, 18:34:46 UTC
630d266 Shaun Adkins 10 December 2018, 18:31:41 UTC take 4 on fixing chado_record_uniq 10 December 2018, 18:31:41 UTC
32c22a2 Shaun Adkins 10 December 2018, 18:30:51 UTC take 4 on fixing chado_record_uniq 10 December 2018, 18:30:51 UTC
d40309e Shaun Adkins 10 December 2018, 18:21:52 UTC take 3 on fixing chado_record_uniq 10 December 2018, 18:21:52 UTC
c6c8762 Shaun Adkins 10 December 2018, 17:08:12 UTC take 3 on fixing chado_record_uniq 10 December 2018, 17:08:12 UTC
62f69ba Shaun Adkins 10 December 2018, 16:46:34 UTC take 3 on fixing chado_record_uniq 10 December 2018, 16:46:34 UTC
601936a Shaun Adkins 10 December 2018, 16:33:57 UTC take 2 on fixing chado_record_uniq 10 December 2018, 16:33:57 UTC
18707d1 Shaun Adkins 10 December 2018, 16:22:35 UTC take 2 on fixing chado_record_uniq 10 December 2018, 16:22:35 UTC
0da97bf Shaun Adkins 10 December 2018, 16:07:22 UTC take 2 on fixing chado_record_uniq 10 December 2018, 16:07:22 UTC
e34788c Shaun Adkins 10 December 2018, 15:52:10 UTC take 2 on fixing chado_record_uniq 10 December 2018, 15:52:10 UTC
9012c41 Shaun Adkins 10 December 2018, 14:54:09 UTC adding LD_LIBRARY_PATH to C Makefile 10 December 2018, 14:54:09 UTC
2f09d16 Shaun Adkins 15 November 2018, 23:21:33 UTC correctly getting ids to map locus tags to 15 November 2018, 23:21:33 UTC
896711e Shaun Adkins 15 November 2018, 22:13:45 UTC edits to pipeline_summary module 15 November 2018, 22:13:45 UTC
9973540 Shaun Adkins 15 November 2018, 20:29:58 UTC adding option in pipeline_summary to use initial gene headers as locustags 15 November 2018, 20:29:58 UTC
c801fe9 Shaun Adkins 15 November 2018, 16:27:05 UTC fixing syntax error 15 November 2018, 16:27:05 UTC
72a3204 Shaun Adkins 15 November 2018, 15:01:13 UTC adding new coordinates file p_func option to pipeline template config 15 November 2018, 15:01:13 UTC
328a9c7 Shaun Adkins 15 November 2018, 15:00:06 UTC adding ability to pass in coordinates file 15 November 2018, 15:00:06 UTC
0b0d9d1 Shaun Adkins 14 November 2018, 20:00:57 UTC adding bsml lookup file to parse evidence configs 14 November 2018, 20:00:57 UTC
901bd5c Shaun Adkins 13 November 2018, 18:40:51 UTC fixing input for 2 components 13 November 2018, 18:40:51 UTC
058c07a Shaun Adkins 13 November 2018, 18:34:59 UTC fixing input for 2 components 13 November 2018, 18:34:59 UTC
3a83370 Shaun Adkins 13 November 2018, 18:17:17 UTC removing unnecessary echo command 13 November 2018, 18:17:17 UTC
57cbb6e Shaun Adkins 08 November 2018, 16:04:05 UTC fixing bad param 08 November 2018, 16:04:05 UTC
ece14bd Shaun Adkins 07 November 2018, 19:38:38 UTC fixing glimmer output name 07 November 2018, 19:38:38 UTC
66a4e74 Shaun Adkins 07 November 2018, 19:14:48 UTC removing pmarks2bsml again and rewriting coords_to_glimmer3 workflow 07 November 2018, 19:14:48 UTC
5877253 Shaun Adkins 07 November 2018, 18:59:17 UTC removing pmarks2bsml again and rewriting coords_to_glimmer3 workflow 07 November 2018, 18:59:17 UTC
72fd7f3 Shaun Adkins 07 November 2018, 16:47:18 UTC fixing variable mismatches 07 November 2018, 16:47:18 UTC
e134521 Shaun Adkins 07 November 2018, 16:25:58 UTC changing component order in pipeline 07 November 2018, 16:25:58 UTC
817923f Shaun Adkins 07 November 2018, 16:06:42 UTC adding new workflow step to coords_to_glimmer3 07 November 2018, 16:06:42 UTC
09c2d3f Shaun Adkins 07 November 2018, 15:29:04 UTC iniitial commit of new pmark finder script 07 November 2018, 15:29:04 UTC
9426934 Shaun Adkins 07 November 2018, 13:45:55 UTC readding pmarks2bsml component 07 November 2018, 13:45:55 UTC
ac1d1d7 Shaun Adkins 06 November 2018, 21:07:48 UTC another config file fix... yay 06 November 2018, 21:07:48 UTC
10a5387 Shaun Adkins 06 November 2018, 20:48:35 UTC fixing input in coords_to_glimmer3 config 06 November 2018, 20:48:35 UTC
374ef46 Shaun Adkins 06 November 2018, 20:39:10 UTC fixing template config file 06 November 2018, 20:39:10 UTC
269f2c4 Shaun Adkins 06 November 2018, 19:49:37 UTC fixing p_func to not use pseudomolecule component 06 November 2018, 19:49:37 UTC
d3fdc61 Shaun Adkins 06 November 2018, 19:47:19 UTC removing pmarks2bsml from pipeline 06 November 2018, 19:47:19 UTC
7196925 Shaun Adkins 06 November 2018, 19:38:37 UTC fixed template to get pipeline to start from script 06 November 2018, 19:38:37 UTC
23c6bb9 Shaun Adkins 06 November 2018, 19:22:39 UTC adding forgotten component 06 November 2018, 19:22:39 UTC
4076b11 Shaun Adkins 06 November 2018, 19:20:22 UTC fixing bug in layout 06 November 2018, 19:20:22 UTC
fb02d1b Shaun Adkins 06 November 2018, 19:00:22 UTC syntax edits to genecalls config script 06 November 2018, 19:00:22 UTC
096b190 Shaun Adkins 06 November 2018, 18:19:58 UTC initial commit of new genecalls v2 pipeline 06 November 2018, 18:19:58 UTC
c059f73 Shaun Adkins 25 October 2018, 13:50:01 UTC Carp module was not imported 25 October 2018, 13:50:01 UTC
222e27b Shaun Adkins 24 October 2018, 15:05:37 UTC fixing path that system looks for wrapper Perl scripts 24 October 2018, 15:05:37 UTC
5baca23 Shaun Adkins 24 October 2018, 14:59:16 UTC changing permisisons 24 October 2018, 14:59:16 UTC
3641225 Shaun Adkins 08 October 2018, 14:33:08 UTC adding LD_LIBRARY_PATH to it's own envvar 08 October 2018, 14:33:08 UTC
5942215 adkinsrs 17 July 2018, 12:41:58 UTC Merge branch 'master' of https://github.com/jorvis/ergatis 17 July 2018, 12:41:58 UTC
2555984 adkinsrs 17 July 2018, 12:41:48 UTC adding pipeline time limit option 17 July 2018, 12:41:48 UTC
ce94d2e Shaun Adkins 05 July 2018, 17:52:12 UTC fixing bug to remove carriage returns 05 July 2018, 17:52:12 UTC
8f354d9 Shaun Adkins 09 April 2018, 16:01:18 UTC added more tests 09 April 2018, 16:01:18 UTC
8f7f866 Shaun Adkins 09 April 2018, 16:00:19 UTC added more tests 09 April 2018, 16:00:19 UTC
57f0994 Shaun Adkins 30 March 2018, 17:40:08 UTC added checks for bsml sequences 30 March 2018, 17:40:08 UTC
1df5ce6 Shaun Adkins 28 March 2018, 16:11:38 UTC initial commit of diff_BSML_files.pl 28 March 2018, 16:11:38 UTC
2ebdc75 Shaun Adkins 28 March 2018, 16:10:07 UTC initial commit of diff_BSML_files.pl 28 March 2018, 16:10:07 UTC
f8b3a55 Shaun Adkins 28 March 2018, 16:01:54 UTC initial commit of diff_BSML_files.pl 28 March 2018, 16:01:54 UTC
47c1005 Shaun Adkins 28 March 2018, 14:19:46 UTC wrote description for a random utility script 28 March 2018, 14:19:46 UTC
4371459 Shaun Adkins 16 March 2018, 14:47:18 UTC modified GFF3 file to be one file instead of multiple 16 March 2018, 14:47:18 UTC
0d524ae Shaun Adkins 12 March 2018, 20:24:54 UTC removing _new from copied filename 12 March 2018, 20:24:54 UTC
b361ba0 Shaun Adkins 09 February 2018, 16:56:53 UTC removing crap from script 09 February 2018, 16:56:53 UTC
36e72dc Shaun Adkins 29 January 2018, 20:31:51 UTC adding checks to ensure paths exist 29 January 2018, 20:31:51 UTC
0641cef Shaun Adkins 29 January 2018, 17:08:53 UTC uncommenting lines, per suvvi's request 29 January 2018, 17:08:53 UTC
672f4e0 Shaun Adkins 24 January 2018, 18:26:18 UTC adding quotes to tbl2asn options in config 24 January 2018, 18:26:18 UTC
790fc32 Shaun Adkins 22 January 2018, 21:22:44 UTC corrected syntax bug 22 January 2018, 21:22:44 UTC
0e9d3f4 Shaun Adkins 22 January 2018, 17:34:38 UTC temporarily commenting out code at Suvvi's request 22 January 2018, 17:34:38 UTC
6d4d739 Shaun Adkins 06 January 2018, 02:47:37 UTC caught issue where hmmpfam3 input reverted back to pre-filtered input before filter_bogus_genes 06 January 2018, 02:47:37 UTC
e1ef061 Shaun Adkins 03 January 2018, 19:48:30 UTC updating code to log correctly upon a 302 Found HTTP Response status 03 January 2018, 19:48:30 UTC
back to top