 Charles Reid
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b0b7a75e44
|
Updating Snakefile to look more like snakemake-rules
|
7 years ago |
|
Charles Reid
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8b919b0e97
|
simplify snakemfile
|
7 years ago |
|
Charles Reid
|
8da83409ca
|
Merge branch 'master' of github.com:charlesreid1/dahak-flot
* 'master' of github.com:charlesreid1/dahak-flot:
update dahak-yeti links
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7 years ago |
|
Charles Reid
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395b9231a9
|
adding info on how to customize the snakemake workflow
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7 years ago |
|
Charles Reid
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5523cc0d49
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Removing cloud from dahak-flot (see dahak-bespin)
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7 years ago |
|
Charles Reid
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c29bacbb01
|
Updating Snakefile onsuccess rule
|
7 years ago |
|
Charles Reid
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2b4f26db87
|
update dahak-yeti links
|
7 years ago |
|
Charles Reid
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74edfa93d7
|
Removing rules that have been moved to the `rules/` directory.
|
7 years ago |
|
Charles Reid
|
c0e4292798
|
do not auto shutdown with user data scriptg
|
7 years ago |
|
Charles Reid
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78c0371671
|
Moving rules to own directory
|
7 years ago |
|
Charles Reid
|
36725beaa5
|
Organizing spy script to be more clear
|
7 years ago |
|
Charles Reid
|
2352d9ff7f
|
yet another subtle networking step - dns.
|
7 years ago |
|
Charles Reid
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15cd129d53
|
Add scripts to make VPC and to make Spy node.
|
7 years ago |
|
Charles Reid
|
d9949b4010
|
make repairs. souped up.
|
7 years ago |
|
Charles Reid
|
3185dc33b9
|
boto VPC script
|
7 years ago |
|
Charles Reid
|
08c5715b10
|
Splitting snakefile out into separate atomic rule files
|
7 years ago |
|
Charles Reid
|
07342b60d8
|
Elminate redundant variables
|
7 years ago |
|
Charles Reid
|
a7b31b1f50
|
Removing data directories for each step.
|
7 years ago |
|
Charles Reid
|
05e76eca19
|
updating organized readme
|
7 years ago |
|
Charles Reid
|
1cfb4e45f7
|
up to and thru kaiju2krona summary completed
|
7 years ago |
|
Charles Reid
|
3f02ba538b
|
add kaiju2krona test
|
7 years ago |
|
Charles Reid
|
c9a7c13caa
|
kaiju2krona rule: wildcard fixes
|
7 years ago |
|
Charles Reid
|
634b19077f
|
Merge branch 'master' of https://github.com/charlesreid1/dahak-flot
|
7 years ago |
|
Charles Reid
|
5867821dbc
|
add run kaiju test and fixes
|
7 years ago |
|
Charles Reid
|
ba22001f0f
|
Update Organized.md
|
7 years ago |
|
Charles Reid
|
f3dab5301a
|
Update Organized.md
|
7 years ago |
|
Charles Reid
|
93ac88cfaf
|
add unpack kaiju to tests
|
7 years ago |
|
Charles Reid
|
be123418cf
|
Unpack kaiju is ok
|
7 years ago |
|
Charles Reid
|
8efd1d0df6
|
Merge branch 'master' of https://github.com/charlesreid1/dahak-flot
|
7 years ago |
|
Charles Reid
|
471648ad3b
|
bootstrap our way to Snakemake
|
7 years ago |
|
Charles Reid
|
c11f2be07f
|
Tested kaiju download
|
7 years ago |
|
Charles Reid
|
7f9f9b3766
|
Update comments
|
7 years ago |
|
Charles Reid
|
9b4d9a7ebc
|
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
|
7 years ago |
|
Charles Reid
|
3df98c487d
|
repair rule to download SBTs.
|
7 years ago |
|
Charles Reid
|
a9855362da
|
Add test script, get Snakefile successfully parsed
|
7 years ago |
|
Charles Reid
|
869a41a027
|
add sample user settings file
|
7 years ago |
|
Charles Reid
|
4dd09035b8
|
getcwd() not get_cwd()
|
7 years ago |
|
Charles Reid
|
0498ed6801
|
fix typo
|
7 years ago |
|
Charles Reid
|
353d3d67ee
|
minor fixes/reordering to getting started doc
|
7 years ago |
|
Charles Reid
|
946968de26
|
Move basic environment yml file
|
7 years ago |
|
Charles Reid
|
7b952fddf5
|
remove unused settings file
|
7 years ago |
|
Charles Reid
|
e3e8fbaa2b
|
update conda command to use yml in envs/
|
7 years ago |
|
Charles Reid
|
f4605ce364
|
Adding kaiju2krona, filter taxa, and visualize krona rules
|
7 years ago |
|
Charles Reid
|
840c5541da
|
Change two hard-coded filenames to variables
|
7 years ago |
|
Charles Reid
|
52836c2971
|
Fix variable scope in run_kaiju rule
|
7 years ago |
|
Charles Reid
|
c8c5c37050
|
Commit an improved Snakefile style. Partially tested.
|
7 years ago |
|
Charles Reid
|
cad22f1331
|
yml, not yaml
|
7 years ago |
|
Charles Reid
|
4fb5259777
|
add link to snakemake examples in the main readme
|
7 years ago |
|
Charles Reid
|
ed7d1a5eac
|
Give attribution to Luiz and snakemake-rules repo
|
7 years ago |
|
Charles Reid
|
fd49e9dfd6
|
Snakefile should use values from a settings file
|
7 years ago |
