| 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 |
| f0c840d | Chris Rosenthal | 18 October 2016, 21:17:25 UTC | some refactoring for clarity | 18 October 2016, 21:17:25 UTC |
| a893f7a | Chris Rosenthal | 14 October 2016, 23:01:58 UTC | making this less noisy | 14 October 2016, 23:01:58 UTC |
| 094ec10 | Chris Rosenthal | 13 October 2016, 23:22:34 UTC | Merge branch 'master' of github.com:fhcrc/deenurp | 13 October 2016, 23:22:34 UTC |
| b5d2f36 | Chris Rosenthal | 13 October 2016, 23:22:12 UTC | adding a function that makes sure the data returned is in utf8 format | 13 October 2016, 23:22:12 UTC |
| 2426b69 | Chris Rosenthal | 05 October 2016, 20:42:56 UTC | added --out_notmatched_taxids | 05 October 2016, 20:42:56 UTC |
| c901c13 | Chris Rosenthal | 27 September 2016, 18:27:28 UTC | correctly feeding arguments to subprocess | 27 September 2016, 18:27:28 UTC |
| 3383d46 | Chris Rosenthal | 26 September 2016, 22:58:44 UTC | no buffering on log file | 26 September 2016, 22:58:44 UTC |
| 530d58e | Chris Rosenthal | 26 September 2016, 22:46:43 UTC | Merge branch 'master' of github.com:fhcrc/deenurp | 26 September 2016, 22:46:43 UTC |
| 55d044b | Chris Rosenthal | 26 September 2016, 22:46:33 UTC | set index after reading csv or dtype will be inferred | 26 September 2016, 22:46:33 UTC |
| 5947aa8 | Chris Rosenthal | 26 September 2016, 22:27:19 UTC | join taxonomy if given | 26 September 2016, 22:27:19 UTC |
| 6edf3da | Chris Rosenthal | 26 September 2016, 21:28:09 UTC | an additional debug log message for tracing tax_id and aligner | 26 September 2016, 21:28:09 UTC |
| 4eccef0 | Chris Rosenthal | 26 September 2016, 17:31:56 UTC | for orientating sequences hopefully 5 rejects is enough | 26 September 2016, 17:31:56 UTC |
| 0984bf0 | Chris Rosenthal | 08 September 2016, 16:52:37 UTC | check if previous_details actually has data in the file | 08 September 2016, 16:52:37 UTC |
| f923c21 | Chris Rosenthal | 07 September 2016, 17:18:02 UTC | Merge branch 'master' of github.com:fhcrc/deenurp | 07 September 2016, 17:18:02 UTC |
| d421bb2 | Chris Rosenthal | 07 September 2016, 17:17:56 UTC | save exception after reading it | 07 September 2016, 17:17:56 UTC |
| 3c627f5 | Noah Hoffman | 02 September 2016, 23:34:54 UTC | Update README.rst | 02 September 2016, 23:34:54 UTC |
| cc941be | Noah Hoffman | 25 August 2016, 20:24:49 UTC | update changelog | 25 August 2016, 20:24:49 UTC |
| b551ecc | Noah Hoffman | 25 August 2016, 20:21:35 UTC | catch ValueError raised by missing parent | 25 August 2016, 20:21:35 UTC |
| 117bfcc | Noah Hoffman | 25 August 2016, 20:21:05 UTC | fix vsearch version check, advance vsearch version | 25 August 2016, 20:21:05 UTC |
| 56021c0 | Noah Hoffman | 25 August 2016, 18:35:43 UTC | update versions of some requirements | 25 August 2016, 18:35:43 UTC |
| 4d9738e | Noah Hoffman | 25 August 2016, 18:35:20 UTC | installs deenurp to virtualenv using -e | 25 August 2016, 18:35:20 UTC |
| 6b4929a | Chris Rosenthal | 22 June 2016, 22:34:36 UTC | remove .ssi to start and end | 22 June 2016, 22:34:56 UTC |
| b676dc7 | Chris Rosenthal | 22 June 2016, 17:09:17 UTC | remove .ssi file at end | 22 June 2016, 17:09:17 UTC |
| 97eac34 | Chris Rosenthal | 16 June 2016, 20:45:49 UTC | output_fp now required --output-seq | 16 June 2016, 20:45:49 UTC |
| 76a5f64 | Chris Rosenthal | 16 June 2016, 18:07:38 UTC | args.log is an actual file now | 16 June 2016, 18:07:38 UTC |
| ec5ae58 | Chris Rosenthal | 14 June 2016, 17:48:52 UTC | --seq-info-out was moved to derep-map-out and replaced with an actual seqinfo file | 14 June 2016, 17:48:52 UTC |
| 008cffc | Chris Rosenthal | 10 June 2016, 23:25:17 UTC | rearranging version numbers to reflect retro release | 10 June 2016, 23:25:17 UTC |
| 8412658 | Chris Rosenthal | 10 June 2016, 22:30:32 UTC | quiet=True vsearch clustering | 10 June 2016, 22:30:32 UTC |
| 6c6926a | Chris Rosenthal | 10 June 2016, 22:23:57 UTC | made a note about deenurp ncbi_extract_genbank max_retry=10 | 10 June 2016, 22:23:57 UTC |
| 24dab6c | Chris Rosenthal | 10 June 2016, 17:43:55 UTC | Merge pull request #56 from fhcrc/054-dereplicate-refs Looks great. All checks have passed. New release? | 10 June 2016, 17:43:55 UTC |
