| e6b2972 | Chris Rosenthal | 04 April 2022, 22:01:51 UTC | fixed url to point to deenurp | 04 April 2022, 22:01:51 UTC |
| 4f7bda5 | Chris Rosenthal | 04 April 2022, 18:20:39 UTC | using default base context | 04 April 2022, 18:20:39 UTC |
| a4a734a | Chris Rosenthal | 04 April 2022, 18:19:07 UTC | Auto build docker image | 04 April 2022, 18:19:07 UTC |
| 22d2bec | Chris Rosenthal | 25 March 2022, 16:10:32 UTC | type: nghoffman | 25 March 2022, 16:10:32 UTC |
| b440541 | Chris Rosenthal | 25 March 2022, 16:07:53 UTC | switching to nhoffman deenurp:0.3.0 image | 25 March 2022, 16:07:53 UTC |
| a51a220 | Chris Rosenthal | 23 March 2022, 17:18:46 UTC | Cleaning up GH Actions yml files | 23 March 2022, 17:18:46 UTC |
| 266e382 | Chris Rosenthal | 23 March 2022, 17:03:47 UTC | removing travis testing | 23 March 2022, 17:03:47 UTC |
| 39350c3 | Chris Rosenthal | 22 March 2022, 22:56:24 UTC | Using deenurp image on unittests | 22 March 2022, 22:56:24 UTC |
| 326661a | Chris Rosenthal | 17 March 2022, 19:03:50 UTC | combining runs | 17 March 2022, 19:03:50 UTC |
| bda544e | Chris Rosenthal | 17 March 2022, 19:01:58 UTC | tests using GH Actions | 17 March 2022, 19:01:58 UTC |
| c9f2266 | Chris Rosenthal | 15 March 2022, 22:09:56 UTC | ignore src dir | 15 March 2022, 22:09:56 UTC |
| 54637a4 | Noah Hoffman | 11 March 2022, 06:19:09 UTC | script to build singularity image | 11 March 2022, 06:19:09 UTC |
| af823fc | Chris Rosenthal | 07 March 2022, 23:22:53 UTC | 070 python3 (#71) 0.3.0 release | 07 March 2022, 23:22:53 UTC |
| ae7dc5b | crosenth | 29 September 2019, 21:23:00 UTC | v0.2.7 release | 29 September 2019, 21:23:00 UTC |
| aecfe48 | crosenth | 29 September 2019, 21:09:21 UTC | Squashed commit of the following: commit e97841638556495e492ad274b315c5b1f580c881 Merge: 6cf8e65 e1ee0ac Author: crosenth <crosenth@uw.edu> Date: Thu Sep 26 14:26:56 2019 -0700 merge with master commit 6cf8e6591c05eeb5f53a28559b81379e7404a140 Merge: 316dfe5 06601ab Author: crosenth <crosenth@uw.edu> Date: Wed May 22 09:51:33 2019 -0700 Merge branch 'master' into replace_peasel commit 316dfe5eabf11880bdab74b13258670131032ecf Author: Chris Rosenthal <crosenth@uw.edu> Date: Mon Dec 17 11:52:37 2018 -0800 enabling tests/run.sh commit ddb37ee40c21a21ef3e66eb96f61ce8443f32545 Author: Chris Rosenthal <crosenth@uw.edu> Date: Mon Dec 17 11:50:58 2018 -0800 removing peasel requirement commit e4118d439e49adc0c4e870824f4ab96f3b94dbb7 Author: Chris Rosenthal <crosenth@uw.edu> Date: Mon Dec 17 11:46:23 2018 -0800 trying to make this work commit 61e48bfa308c39378ee17a51c3f037981c6ab85a Author: Chris Rosenthal <crosenth@uw.edu> Date: Wed Dec 12 14:48:20 2018 -0800 forgot to add that second argument to SeqIO commit b0610e73c67d44866ccd2574bd3baf64612d68d6 Author: Chris Rosenthal <crosenth@uw.edu> Date: Wed Dec 12 14:42:11 2018 -0800 updated all references to esl_sfetch commit 287392f17ae94ff50aba8514840039f470b0a819 Author: Chris Rosenthal <crosenth@uw.edu> Date: Tue Dec 11 16:23:03 2018 -0800 remove peasel requirement by reading fasta file and recording binary offset location of each fasta sequence commit cc7a611b3ef2f0d14797bb535505861c70279958 Author: Chris Rosenthal <crosenth@uw.edu> Date: Wed Dec 5 10:20:47 2018 -0800 beta release of peasel replacement | 29 September 2019, 21:09:21 UTC |
| e1ee0ac | crosenth | 07 June 2019, 23:24:41 UTC | v0.2.6 | 07 June 2019, 23:24:41 UTC |
| 65b9753 | crosenth | 06 June 2019, 22:32:58 UTC | removed the wait keyword | 06 June 2019, 22:32:58 UTC |
| 471c627 | crosenth | 06 June 2019, 22:26:52 UTC | do not need the 60 second timeout anymore | 06 June 2019, 22:26:52 UTC |
| 63815fd | crosenth | 06 June 2019, 22:25:59 UTC | converting two lists to sets to speed up searching | 06 June 2019, 22:25:59 UTC |
| 06601ab | Chris Rosenthal | 05 December 2018, 22:58:53 UTC | moving images to 18.04 and building Singularity image from Singularity build file | 05 December 2018, 22:58:53 UTC |
| 2d5bd47 | Chris Rosenthal | 05 December 2018, 18:23:21 UTC | update CHANGES log | 05 December 2018, 18:23:21 UTC |
| 07a9d17 | Chris Rosenthal | 04 December 2018, 22:00:08 UTC | raising to 3 sequence minimum for fasttree | 04 December 2018, 22:00:08 UTC |
| 853b4a7 | Chris Rosenthal | 04 December 2018, 00:29:19 UTC | filter_outliers --no-filter argument | 04 December 2018, 00:29:19 UTC |
| 52495db | Noah Hoffman | 01 October 2018, 16:52:43 UTC | update changelog | 01 October 2018, 16:52:43 UTC |
| f506a4d | Noah Hoffman | 01 October 2018, 16:51:33 UTC | raise ValueError when < 3 sequences are provided to fasttree | 01 October 2018, 16:51:33 UTC |
| 2531385 | Noah Hoffman | 01 October 2018, 16:51:04 UTC | fix error when query and ref seqs have name collision | 01 October 2018, 16:51:04 UTC |
| 38484bb | Chris Rosenthal | 12 April 2018, 19:57:55 UTC | fixed some Pyhton Pandas warnings | 12 April 2018, 19:57:55 UTC |
| fd27ec2 | Noah Hoffman | 08 January 2018, 23:22:13 UTC | update changelog | 08 January 2018, 23:22:13 UTC |
| 8e76eb9 | Noah Hoffman | 08 January 2018, 23:09:23 UTC | just test cmalign in filter_outliers | 08 January 2018, 23:09:23 UTC |
| 101bdad | Noah Hoffman | 08 January 2018, 22:29:26 UTC | purge fewer libraries | 08 January 2018, 22:29:26 UTC |
| 1cb4ec6 | Noah Hoffman | 08 January 2018, 22:23:07 UTC | fix typo in package name | 08 January 2018, 22:23:07 UTC |
| 81b04ed | Noah Hoffman | 08 January 2018, 21:39:26 UTC | purge more things | 08 January 2018, 21:39:26 UTC |
| 6ae9453 | Noah Hoffman | 08 January 2018, 21:27:38 UTC | clean up apt sources and run complete test suite | 08 January 2018, 21:32:10 UTC |
| a889577 | Noah Hoffman | 08 January 2018, 21:20:17 UTC | update dependencies | 08 January 2018, 21:20:17 UTC |
| 7424615 | Noah Hoffman | 08 January 2018, 20:12:40 UTC | back to 16.04 | 08 January 2018, 20:12:40 UTC |
| 9a9a4e0 | Noah Hoffman | 08 January 2018, 20:07:43 UTC | run apt-get update | 08 January 2018, 20:07:43 UTC |
| 9b26be7 | Noah Hoffman | 08 January 2018, 20:06:06 UTC | try importing from python:2.7.14-stretch | 08 January 2018, 20:06:06 UTC |
| b78d83a | Noah Hoffman | 08 January 2018, 19:52:11 UTC | don't apt-get update in docker image | 08 January 2018, 19:52:11 UTC |
| 850a1a2 | Noah Hoffman | 08 January 2018, 19:48:06 UTC | run tests using python -m deenurp.test | 08 January 2018, 19:48:06 UTC |
| 9d6a8b7 | Noah Hoffman | 08 January 2018, 00:27:14 UTC | skip some tests when dependencies are missing | 08 January 2018, 00:27:14 UTC |
| 78997a1 | Noah Hoffman | 27 November 2017, 21:29:22 UTC | update changelog | 27 November 2017, 21:29:22 UTC |
| 2518be3 | Noah Hoffman | 27 November 2017, 21:26:59 UTC | create some additional mounpoints in Docker image | 27 November 2017, 21:27:12 UTC |
| 93ece69 | Noah Hoffman | 27 November 2017, 21:24:36 UTC | update taxtastic to 0.8.3 | 27 November 2017, 21:24:36 UTC |
| eb90e47 | Noah Hoffman | 27 November 2017, 21:20:39 UTC | install seqmagick | 27 November 2017, 21:20:39 UTC |
| dfe765a | Noah Hoffman | 25 October 2017, 04:40:06 UTC | update changelog | 25 October 2017, 04:40:06 UTC |
| 587e489 | Noah Hoffman | 25 October 2017, 04:05:54 UTC | fix git versioning | 25 October 2017, 04:08:16 UTC |
| 288afb5 | Noah Hoffman | 23 October 2017, 23:44:16 UTC | add Singularity build scripts | 23 October 2017, 23:44:16 UTC |
| 162f74d | Noah Hoffman | 23 October 2017, 22:15:10 UTC | ignore *.pyc in with .dockerignore | 23 October 2017, 22:15:10 UTC |
| b17e0ab | Noah Hoffman | 23 October 2017, 21:28:30 UTC | update changelog | 23 October 2017, 21:28:30 UTC |
| 39ce1fc | Noah Hoffman | 23 October 2017, 21:26:40 UTC | Merge branch 'master' into sminot-dockerfile Conflicts: deenurp/wrap.py | 23 October 2017, 21:26:40 UTC |
| d167466 | Chris Rosenthal | 20 October 2017, 20:00:47 UTC | Merge branch 'master' of github.com:fhcrc/deenurp | 20 October 2017, 20:00:47 UTC |
| f159e9e | Noah Hoffman | 17 October 2017, 05:53:38 UTC | fix error parsing cmalign scores file | 17 October 2017, 05:54:13 UTC |
| d1af93d | Chris Rosenthal | 10 October 2017, 23:47:34 UTC | hiding vsearch --version stdout | 10 October 2017, 23:47:34 UTC |
| 4d38693 | Chris Rosenthal | 10 October 2017, 23:03:59 UTC | using latest versions of taxtastic, vsearch and virtualenv | 10 October 2017, 23:03:59 UTC |
| a80badf | Chris Rosenthal | 10 October 2017, 19:40:13 UTC | deenurp must be installed to python2.7/lib/site-packages to work with Singularity | 10 October 2017, 19:40:13 UTC |
| 817963a | Chris Rosenthal | 10 October 2017, 18:57:26 UTC | building venv into /usr/local/ | 10 October 2017, 18:57:26 UTC |
| 9212408 | Chris Rosenthal | 10 October 2017, 18:04:19 UTC | ADD-ing only necessary directories and files | 10 October 2017, 18:04:19 UTC |
| a29d64f | Chris Rosenthal | 10 October 2017, 18:03:52 UTC | allow make 4 jobs and added a couple echo messages | 10 October 2017, 18:03:52 UTC |
| 96176a7 | Chris Rosenthal | 10 October 2017, 18:02:17 UTC | remove pyc files before building docker image | 10 October 2017, 18:02:17 UTC |
| d34dc56 | Noah Hoffman | 09 October 2017, 20:49:40 UTC | todos in dockerfile | 09 October 2017, 20:49:40 UTC |
| 4a704a4 | Noah Hoffman | 09 October 2017, 20:46:47 UTC | increase singularity image size | 09 October 2017, 20:47:02 UTC |
| d136726 | Noah Hoffman | 09 October 2017, 20:35:02 UTC | wget instead of curl | 09 October 2017, 20:35:02 UTC |
| ba9dc93 | Noah Hoffman | 09 October 2017, 20:30:35 UTC | build scripts for docker and sigularity | 09 October 2017, 20:30:35 UTC |
| de14a5c | Chris Rosenthal | 29 September 2017, 18:13:51 UTC | removing gi references | 29 September 2017, 18:13:51 UTC |
| 66650e1 | Noah Hoffman | 29 September 2017, 04:58:08 UTC | install pysqlite (for taxtastic) | 29 September 2017, 04:58:08 UTC |
| 3b4e822 | Noah Hoffman | 29 September 2017, 00:01:24 UTC | update dockerfile - bootstrap.sh installs python dependencies - update requirements | 29 September 2017, 00:01:24 UTC |
| 9596f22 | Noah Hoffman | 28 September 2017, 23:46:57 UTC | remove rdp_extract_genbank subcommand | 28 September 2017, 23:46:57 UTC |
| 61f6fba | Noah Hoffman | 28 September 2017, 23:34:40 UTC | remove tax2tree subcommand and dependencies | 28 September 2017, 23:34:40 UTC |
| 812a828 | Sam Minot | 21 September 2017, 19:53:30 UTC | Default path is `bin-env` | 21 September 2017, 19:53:30 UTC |
| 05a1d72 | Sam Minot | 21 September 2017, 19:52:30 UTC | Switch to pypi from github | 21 September 2017, 19:52:30 UTC |
| dfaf834 | Sam Minot | 21 September 2017, 04:39:20 UTC | Add dockerfile | 21 September 2017, 04:39:20 UTC |
| 7b3ae87 | Noah Hoffman | 19 September 2017, 00:15:15 UTC | don't hard-code path to python2.7 | 19 September 2017, 00:15:15 UTC |
| caf764c | Chris Rosenthal | 15 September 2017, 00:27:01 UTC | use /usr/local/bin/python2.7 for virtualenv | 15 September 2017, 00:27:01 UTC |
| 4a25f6d | Noah Hoffman | 03 August 2017, 17:46:27 UTC | fix edge case in which too many refs are lost by clustering | 03 August 2017, 17:46:27 UTC |
| 833e14d | Chris Rosenthal | 26 June 2017, 16:57:12 UTC | requires latest taxtastic version v0.6.4 | 26 June 2017, 16:57:12 UTC |
| b36ba59 | Chris Rosenthal | 14 June 2017, 16:39:15 UTC | need the cluster column from previous_details | 14 June 2017, 16:39:15 UTC |
| 9c1a7f5 | Chris Rosenthal | 12 June 2017, 23:57:21 UTC | do not try to interpret datatypes in seq_info, just take everything as a string | 12 June 2017, 23:57:21 UTC |
| e6bf6a5 | Chris Rosenthal | 12 June 2017, 22:03:03 UTC | Merge branch 'master' of github.com:fhcrc/deenurp | 12 June 2017, 22:03:03 UTC |
| 8c8748a | Chris Rosenthal | 12 June 2017, 22:02:52 UTC | replace "/" in temporary filenames because it confuses the filesystem | 12 June 2017, 22:02:52 UTC |
| bf5e670 | Chris Rosenthal | 01 June 2017, 19:19:09 UTC | use subtree_sequence_ids() to get all sequences below filter_rank | 01 June 2017, 19:19:09 UTC |
| d95eec0 | Chris Rosenthal | 31 May 2017, 21:20:51 UTC | Merge branch 'master' of github.com:fhcrc/deenurp | 31 May 2017, 21:20:51 UTC |
| e4d4510 | Chris Rosenthal | 31 May 2017, 21:20:43 UTC | moving this into its specific pipeline | 31 May 2017, 21:20:43 UTC |
| 7154d28 | Chris Rosenthal | 12 May 2017, 21:30:13 UTC | make sure all sequences are accounted for before clustering begins | 12 May 2017, 21:30:13 UTC |
| 386a6e2 | Chris Rosenthal | 01 May 2017, 23:25:09 UTC | moving this functionality into the pipeline it was designed for | 01 May 2017, 23:25:09 UTC |
| 7316723 | Chris Rosenthal | 26 April 2017, 23:55:35 UTC | use latest virtualenv and specify python2 | 26 April 2017, 23:55:35 UTC |
| cf6cdaa | Chris Rosenthal | 21 April 2017, 20:55:23 UTC | moving these subcommands directly into their respected pipelines | 21 April 2017, 20:55:23 UTC |
| 0008046 | Chris Rosenthal | 07 April 2017, 23:02:07 UTC | some syntax updating | 07 April 2017, 23:02:07 UTC |
| fd9e503 | Noah Hoffman | 30 March 2017, 22:41:17 UTC | fix error in select_references when using --include-clusters select_sequences_for_whitelist_cluster() returned a set of seq_ids instead of a list of SeqRecord() | 30 March 2017, 22:41:17 UTC |
| 4ab7f68 | Noah Hoffman | 30 March 2017, 22:14:27 UTC | update help text for select_references - add metavars to clarify input types - raise NotImplementedError for select('include_sequences') | 30 March 2017, 22:14:27 UTC |
| 2d3371b | Chris Rosenthal | 10 January 2017, 18:59:52 UTC | using regular esearch and not record gi numbers | 10 January 2017, 18:59:52 UTC |
| 9afc166 | Chris Rosenthal | 05 January 2017, 22:37:57 UTC | merge conficts | 05 January 2017, 22:37:57 UTC |
| 052b0dd | Chris Rosenthal | 05 January 2017, 22:36:41 UTC | do not modify shebang lines | 05 January 2017, 22:36:41 UTC |
| cee48a5 | Chris Rosenthal | 05 January 2017, 21:46:56 UTC | specify pip2 for installing | 05 January 2017, 21:46:56 UTC |
| d541b55 | Chris Rosenthal | 06 December 2016, 20:17:43 UTC | do not sniff gi numbers | 06 December 2016, 20:17:43 UTC |
| d75df59 | Chris Rosenthal | 23 November 2016, 20:04:23 UTC | gi number is a string | 23 November 2016, 20:04:23 UTC |
| 63584b2 | Chris Rosenthal | 04 November 2016, 21:58:55 UTC | output seq_info with same columns as input seq_info | 04 November 2016, 21:58:55 UTC |
| aba0dd3 | Chris Rosenthal | 28 October 2016, 20:26:59 UTC | Merge branch 'master' of github.com:fhcrc/deenurp | 28 October 2016, 20:26:59 UTC |
| eec7cfb | Chris Rosenthal | 28 October 2016, 20:26:47 UTC | import subcommands only when needed by parse_subcommands | 28 October 2016, 20:26:47 UTC |
| 8c188f4 | Chris Rosenthal | 24 October 2016, 21:29:52 UTC | check for three colons in features input | 24 October 2016, 21:29:52 UTC |
| 5938f54 | Chris Rosenthal | 18 October 2016, 21:17:41 UTC | cleaned up write_or_append | 18 October 2016, 21:17:41 UTC |
