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Running PR for Snakemakeification #164

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Running PR for Snakemakeification #164

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e887d2a
add rename and stats components
camillescott Nov 7, 2019
0b4ce27
add remap hmmer component
camillescott Nov 7, 2019
daf61bf
remove converted tasks
camillescott Nov 7, 2019
f28101e
move busco parsers to fileio submodule
camillescott Nov 7, 2019
4e0207a
convert and filter components
camillescott Nov 7, 2019
fcf9d04
Add conversion components
camillescott Nov 7, 2019
a37d5dd
Get gff3 merge command working
camillescott Nov 7, 2019
6293805
add busco, transdecoder wrappers
bluegenes Nov 7, 2019
b562c25
ADd annotate component
camillescott Nov 7, 2019
06fd042
Merge branch 'decompose' of github.com:camillescott/dammit into decom…
camillescott Nov 7, 2019
bb4b203
add rename-transcriptome wrapper
camillescott Nov 7, 2019
56ce4b7
add transdecoder test data, rules
bluegenes Nov 8, 2019
8a595bb
add busco rule, busco testdata
bluegenes Nov 8, 2019
6165178
add last
bluegenes Nov 8, 2019
d4f7bf1
add infernal wrapper and rule
bluegenes Nov 8, 2019
cdaf6ec
First round of workflow structuring: database download
camillescott Nov 13, 2019
accacaf
merge download rules
camillescott Nov 13, 2019
9f719eb
add transdecoder, last, infernal, hmmer wrappers
bluegenes Nov 15, 2019
388ce3e
init hmmer, transdecoder workflows
bluegenes Nov 16, 2019
86c25c3
code removal
camillescott Dec 2, 2019
0edabeb
Merge branch 'decompose' of github.com:camillescott/dammit into decom…
camillescott Dec 2, 2019
fd22338
add yaml; init annot snakes
bluegenes Dec 10, 2019
06b5ab6
init config changes; init main snake
bluegenes Dec 10, 2019
aa11da7
yml db file
bluegenes Dec 10, 2019
2778bea
Merge branch 'decompose' of github.com:camillescott/dammit into decom…
camillescott Dec 12, 2019
e111db1
working snakemake calls
bluegenes Dec 15, 2019
2429aaf
fix md5 downloads
bluegenes Dec 15, 2019
654d4a8
ignore metalink for now
bluegenes Dec 15, 2019
faa5671
fix lastdb wrapper
bluegenes Dec 15, 2019
a5564b8
working transdecoder
bluegenes Dec 16, 2019
c4c48a6
getting... closer...
bluegenes Dec 16, 2019
264d037
init env
bluegenes Dec 16, 2019
41b304f
Merge branch 'decompose' of github.com:camillescott/dammit into decom…
camillescott Feb 27, 2020
2c59f70
upd busco env and wrapper
bluegenes Feb 27, 2020
0726f2b
Remove cruft; use paths relative to installation dir for config and w…
camillescott Feb 28, 2020
8c36447
Merge branch 'decompose' of github.com:camillescott/dammit into decom…
camillescott Feb 28, 2020
656660c
Get annotate working with install-relative paths and fix some formatt…
camillescott Feb 28, 2020
579253b
Update requirements
camillescott Apr 17, 2020
fb43ee3
init setup snakefile
bluegenes Apr 17, 2020
13b2b98
Remove sphinx
camillescott Apr 17, 2020
0db1612
Remove _build folder
camillescott Apr 17, 2020
0acc86f
add mkdocs to dev reqs
camillescott Apr 17, 2020
33fbbfe
Merge pull request #171 from dib-lab/update_reqs
camillescott Apr 17, 2020
020c1d7
init file conversion rules
bluegenes Apr 18, 2020
6be0cde
add gff3 file targets; fix rename txome wrapper
bluegenes Apr 18, 2020
e3cf8c0
Merge pull request #175 from dib-lab/add_conversion_rules
camillescott Apr 18, 2020
df7457a
init shmlast wrapper, init shmlast and busco-v4 rules
bluegenes Apr 23, 2020
5a82181
Refactor config and add config components
camillescott Apr 24, 2020
4198dac
First pass unifying argparse and click interfaces
camillescott Apr 24, 2020
7ec2089
Add database dir as envvar
camillescott Apr 24, 2020
a4045e7
add .snakemake to gitignore
camillescott Apr 24, 2020
fe8105b
vendor cloup
camillescott Apr 24, 2020
abb3919
Reorganize components into cloup groups
camillescott Apr 24, 2020
7c74df2
Remove busco tasks
camillescott Apr 24, 2020
0c3f2d8
remove tasks suybmodules
camillescott Apr 24, 2020
7fb46ba
Fix regression in remap hmmer
camillescott Apr 24, 2020
de2bd9e
add user db targets; init write config
bluegenes Apr 24, 2020
c7792bb
Nuke the rest of dammit.tasks
camillescott Apr 24, 2020
dda80e9
Strip out more doit utils
camillescott Apr 24, 2020
7c3b10f
add .vscode to gitignore
camillescott Apr 24, 2020
8ac85f5
Add --version switch
camillescott Apr 24, 2020
97df5e3
Remove help from remap hmmer
camillescott Apr 24, 2020
6936544
enable print config
bluegenes Apr 24, 2020
86e545c
fix configfile printing
bluegenes Apr 25, 2020
480e8f6
get dammit databases subcommand working again
camillescott Apr 25, 2020
13bb949
change cmd order
bluegenes Apr 25, 2020
70cf00c
fix configfiles
bluegenes Apr 25, 2020
caecc4a
add shmlast to pipeline yml; fix targeting
bluegenes Apr 26, 2020
1565730
enable busco
bluegenes Apr 27, 2020
5e69a02
upd snkmk
bluegenes Apr 27, 2020
4f0549b
refactor databases target gen
camillescott May 8, 2020
18af046
Bring in busco support
camillescott May 8, 2020
0d5bc54
change busco wrapper to enable config
bluegenes May 8, 2020
c0f34a9
comment out in progress rule
bluegenes May 9, 2020
befe039
Fix generate_annotation_targets, convert annotate to click parsing
camillescott May 9, 2020
cded805
merge in remove_argparse branch
bluegenes May 9, 2020
f1a2fe6
upd busco databases, fix busco targeting in run
bluegenes May 9, 2020
7af8112
fix busco db in run
bluegenes May 9, 2020
ad03bf8
working databases download
bluegenes May 9, 2020
bdd638d
working busco run!
bluegenes May 9, 2020
f0a5fc9
move addl setup rule to new branch
bluegenes May 9, 2020
0e31171
Merge pull request #179 from dib-lab/add_busco_config
camillescott May 15, 2020
ed37c53
Merge pull request #177 from dib-lab/remove_argparse
camillescott May 15, 2020
00bf252
Add in best-hits step and fix database attribute in gff3 outputs
camillescott May 15, 2020
2bf0ea6
seems to be working
bluegenes May 16, 2020
84198d4
Fix file output naming conventions, start migrating config locations
camillescott May 29, 2020
81d7702
fix paths in ini config
bluegenes May 30, 2020
afb883c
Rewire temp folders and add config output subcommands
camillescott May 30, 2020
eac1321
Merge in BUSCO config fixes
camillescott May 30, 2020
17676d0
Add temp directory cleaning command
camillescott May 30, 2020
50d1bd4
Merge pull request #185 from dib-lab/extricate_fileio
camillescott May 30, 2020
9c12e37
add busco plotting
bluegenes May 30, 2020
2d324ac
Merge branch 'decompose' into plot_busco
bluegenes May 30, 2020
0d091bf
message formatting
camillescott Jun 26, 2020
8de727f
Merge pull request #186 from dib-lab/plot_busco
camillescott Jun 26, 2020
c632c2e
Add tests for wrappers and components (#188)
camillescott Aug 7, 2020
4ba07a9
use mamba for conda installations (#193)
bluegenes Aug 7, 2020
d1a450f
Nuke it from orbit: general clean-up and bugfixing (#196)
camillescott Oct 26, 2020
e07d01f
Refactor GFF3 conversion code to fix ID non-determinism with threadin…
camillescott Oct 30, 2020
4ac8af9
Snakefile formatting and file hierarchy cleanup (#201)
camillescott Jan 13, 2021
7031204
Remove busci.ini download as part of databases pipeline.
camillescott Jan 14, 2021
00bf7da
--n-threads can be set by environment variable
camillescott Jan 14, 2021
330626a
Add nice output to run commands
camillescott Jan 15, 2021
7bc1c38
Remove extraneous print
camillescott Jan 22, 2021
40ef4dc
Add an environment variable DAMMIT_TESTING_TEMP_BASE_DIR to set a sta…
camillescott Jan 22, 2021
99a1fbd
Merge pull request #204 from dib-lab/ui_improvements
camillescott Jan 22, 2021
91202b3
Merge pull request #205 from dib-lab/conda_testing_configuration
camillescott Jan 22, 2021
ee58118
Add dammit-transcriptome-stats to annotation workflow
camillescott Jan 23, 2021
38dd482
Add transcriptome_stats task to all pipelines
camillescott Jan 25, 2021
ba4e3e2
add rich to environment requirements
camillescott Jan 25, 2021
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4 changes: 4 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -29,3 +29,7 @@ dammit.egg-info/

.ipynb_checkpoints/
.pytest_cache/

*.snakemake
.vscode/
envs/
96 changes: 0 additions & 96 deletions ChangeLog
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