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• b0b7a75e44 Updating Snakefile to look more like snakemake-rules master Charles Reid 2018-03-21 15:53:59 -07:00
• 8b919b0e97 simplify snakemfile Charles Reid 2018-03-20 12:32:52 -07:00
• 8da83409ca Merge branch 'master' of github.com:charlesreid1/dahak-flot Charles Reid 2018-03-14 18:36:27 -07:00
• 395b9231a9 adding info on how to customize the snakemake workflow Charles Reid 2018-03-14 18:36:12 -07:00
• 5523cc0d49 Removing cloud from dahak-flot (see dahak-bespin) Charles Reid 2018-03-14 18:28:08 -07:00
• c29bacbb01 Updating Snakefile onsuccess rule Charles Reid 2018-03-14 18:27:34 -07:00
• 2b4f26db87
  update dahak-yeti links Chaz Reid 2018-03-14 18:22:15 -07:00
• 74edfa93d7 Removing rules that have been moved to the rules/ directory. Charles Reid 2018-03-12 06:42:29 -07:00
• c0e4292798 do not auto shutdown with user data scriptg Charles Reid 2018-03-09 15:23:07 -08:00
• 78c0371671 Moving rules to own directory Charles Reid 2018-03-09 14:34:36 -08:00
• 36725beaa5 Organizing spy script to be more clear Charles Reid 2018-03-09 14:18:38 -08:00
• 2352d9ff7f yet another subtle networking step - dns. Charles Reid 2018-03-09 14:06:11 -08:00
• 15cd129d53 Add scripts to make VPC and to make Spy node. Charles Reid 2018-03-09 10:08:18 -08:00
• d9949b4010 make repairs. souped up. Charles Reid 2018-03-09 01:15:35 -08:00
• 3185dc33b9 boto VPC script Charles Reid 2018-03-08 23:37:59 -08:00
• 08c5715b10 Splitting snakefile out into separate atomic rule files Charles Reid 2018-03-08 19:24:56 -08:00
• 07342b60d8 Elminate redundant variables Charles Reid 2018-03-08 18:26:31 -08:00
• a7b31b1f50 Removing data directories for each step. Charles Reid 2018-03-08 10:31:33 +00:00
• 05e76eca19 updating organized readme Charles Reid 2018-03-08 10:31:19 +00:00
• 1cfb4e45f7 up to and thru kaiju2krona summary completed Charles Reid 2018-03-08 04:46:23 +00:00
• 3f02ba538b add kaiju2krona test Charles Reid 2018-03-08 02:34:17 +00:00
• c9a7c13caa kaiju2krona rule: wildcard fixes Charles Reid 2018-03-08 02:34:00 +00:00
• 634b19077f Merge branch 'master' of https://github.com/charlesreid1/dahak-flot Charles Reid 2018-03-08 00:55:34 +00:00
• 5867821dbc add run kaiju test and fixes Charles Reid 2018-03-08 00:54:10 +00:00
• ba22001f0f
  Update Organized.md Chaz Reid 2018-03-07 15:57:20 -08:00
• f3dab5301a
  Update Organized.md Chaz Reid 2018-03-07 15:56:41 -08:00
• 93ac88cfaf add unpack kaiju to tests Charles Reid 2018-03-07 23:32:54 +00:00
• be123418cf Unpack kaiju is ok Charles Reid 2018-03-07 23:32:35 +00:00
• 8efd1d0df6 Merge branch 'master' of https://github.com/charlesreid1/dahak-flot Charles Reid 2018-03-07 23:30:40 +00:00
• 471648ad3b bootstrap our way to Snakemake Charles Reid 2018-03-07 15:29:49 -08:00
• c11f2be07f Tested kaiju download Charles Reid 2018-03-07 23:07:57 +00:00
• 7f9f9b3766 Update comments Charles Reid 2018-03-06 09:40:46 +00:00
• 9b4d9a7ebc Verified snakefile up to sourmash step. Charles Reid 2018-03-06 09:36:20 +00:00
• 3df98c487d repair rule to download SBTs. Charles Reid 2018-03-06 02:56:56 +00:00
• a9855362da Add test script, get Snakefile successfully parsed Charles Reid 2018-03-06 02:34:15 +00:00
• 869a41a027 add sample user settings file Charles Reid 2018-03-05 18:22:33 -08:00
• 4dd09035b8 getcwd() not get_cwd() Charles Reid 2018-03-05 18:20:25 -08:00
• 0498ed6801 fix typo Charles Reid 2018-03-05 18:16:09 -08:00
• 353d3d67ee minor fixes/reordering to getting started doc Charles Reid 2018-03-05 18:14:57 -08:00
• 946968de26 Move basic environment yml file Charles Reid 2018-03-05 17:04:41 -08:00
• 7b952fddf5 remove unused settings file Charles Reid 2018-03-05 17:04:17 -08:00
• e3e8fbaa2b update conda command to use yml in envs/ Charles Reid 2018-03-05 17:03:11 -08:00
• f4605ce364 Adding kaiju2krona, filter taxa, and visualize krona rules Charles Reid 2018-03-05 13:00:20 -08:00
• 840c5541da Change two hard-coded filenames to variables Charles Reid 2018-03-02 19:33:56 -08:00
• 52836c2971 Fix variable scope in run_kaiju rule Charles Reid 2018-03-02 16:19:46 -08:00
• c8c5c37050 Commit an improved Snakefile style. Partially tested. Charles Reid 2018-03-02 16:12:26 -08:00
• cad22f1331 yml, not yaml Charles Reid 2018-03-02 16:12:00 -08:00
• 4fb5259777 add link to snakemake examples in the main readme Charles Reid 2018-03-01 10:22:20 -08:00
• ed7d1a5eac
  Give attribution to Luiz and snakemake-rules repo Chaz Reid 2018-02-27 19:41:04 -08:00
• fd49e9dfd6 Snakefile should use values from a settings file Charles Reid 2018-02-27 15:56:19 -08:00
• 4f285fe1cd Update link to snakemake-rules repo Charles Reid 2018-02-27 15:55:49 -08:00
• c8c390dbb9 removing dummy subtask. Charles Reid 2018-02-27 11:14:02 -08:00
• 0786a16fc9 Premature commit - close lambda function Charles Reid 2018-02-27 10:56:28 -08:00
• 88ec6da09f Adding first few rules for tax. class. Snakefile Charles Reid 2018-02-27 10:39:44 -08:00
• a1a4d86e82 Updating notes Charles Reid 2018-02-26 22:07:31 -08:00
• f61ca31923 Improving docs Charles Reid 2018-02-23 16:32:33 -08:00
• 78356b2897 main Snakemake default rule now calls subtask1 rule Charles Reid 2018-02-23 16:31:24 -08:00
• 29da207753 why flot? Charles Reid 2018-02-23 16:10:20 -08:00
• 5da81ff1d4 Adding docs, initial commit of illustrative subtask. Charles Reid 2018-02-23 15:44:17 -08:00
• 51e1376c87 2 legit 2 init commit Charles Reid 2018-02-22 18:06:03 -08:00