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