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Updates and BGC Feature #215

Merged
merged 47 commits into from
Jan 30, 2023
Merged

Updates and BGC Feature #215

merged 47 commits into from
Jan 30, 2023

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matinnuhamunada
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@matinnuhamunada matinnuhamunada commented Dec 21, 2022 •
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  • Update BiG-SCAPE (1.1.5) and MIBIG (3.1) MIBIG 3 on BiG-SCAPE #206
  • Report notebook updates: arts, cblaster, checkm, roary, and eggnog
  • Experimental unit test from Snakemake (automatically generated). Need to know how to recycle existing conda environment for the test, rather than creating a new conda env for each test in /tmp
  • New Features:
    • BGC table can now be accessed Feature: df_bgcs tables with all metadata #197
    • Subworkflow to work with BGCs: interproscan, clinker, bigscape, and bigslice. We have not tested this workflow to run multiple projects. This can be run via: 
      Snakemake --snakefile workflow/BGC --use-conda
    • Experimental docker container hosted in: "docker://matinnu/bgcflow:latest. This are not fully working yet and the size is huge. Containerize workflow #180 
      Snakemake --use-singularity --use-conda
    • Snakefile to start metabase server 
      Snakemake --snakefile workflow/Metabase

@matinnuhamunada matinnuhamunada added the enhancement New feature or request label Dec 21, 2022
@matinnuhamunada matinnuhamunada self-assigned this Dec 21, 2022
@matinnuhamunada matinnuhamunada linked an issue Dec 21, 2022 that may be closed by this pull request
MIBIG 3 on BiG-SCAPE #206
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@matinnuhamunada
fix: correct bgc_ids from ARTS2 table
88ca2f5
@matinnuhamunada
feat: extract bgc table from antismash
2dee08d
@matinnuhamunada
notebook: update checkm figure with MIMAG classification
0f2c62f
@matinnuhamunada
feat: give better flexibility to choose project types
389c8b5
@matinnuhamunada
feat: introduce a bgc project type
4d68caf
@matinnuhamunada
feat: add interproscan and clinker
34f88bc
@matinnuhamunada
fix: correct genome_id naming
81d3fcb
@matinnuhamunada
chore: tidy logging info for gtdbtk and antismash install
ed5a8da
@matinnuhamunada
feat: add experimental Dockerfile
5a35456
@matinnuhamunada
fix: add working Dockerfile and Dockerhub link
4879e9d
@matinnuhamunada
fix: enable multiple bgc_id from the same genome_id
0ecd126
@matinnuhamunada
chore: use input path for variable changelog
56370f1
@matinnuhamunada
feat: add parameter max cluster size for roary
8330ae5
@matinnuhamunada
test: rename to tests to accomodate unit tests
527a330
@matinnuhamunada
test: add arts_extract unit test
f77e3b5
@matinnuhamunada
test: add fix_gtdb_taxonomy test
066674a
@matinnuhamunada
test: add gtdb_prep test
0b09fc1
@matinnuhamunada
fix: add missing config files for tests
6363392
@matinnuhamunada
test: add mash_convert test
e3262fa
@matinnuhamunada
test: add fastani_convert test
2f4dea4
@matinnuhamunada
test: add deeptfactor_to_json test
3f70103
@matinnuhamunada
test: add extract_ncbi_information test
bbd8d68
@matinnuhamunada
test: add antismash_overview_gather test
d6e7f10
@matinnuhamunada
test: remove on-success and try out pytest action
584f772
@matinnuhamunada
test: add coverage report
1d2bc3a
@matinnuhamunada
test: fix coverage report commentator
1ad4d54
@matinnuhamunada
feat: add Snakefile to run Metabase
a3126c1
@matinnuhamunada
fix: stop showing roary plot
68d686b
@matinnuhamunada
notebook: update eggnog reports
9f2de0a
@matinnuhamunada
test: add lactobacillus minimal example
346d0b7
@matinnuhamunada
fix: correct java and perl requirement for interproscan
a41a0ca
@matinnuhamunada
fix: don't include mibig in bigscape for BGCs
beb4dbc
@matinnuhamunada
chore: use conda with JDK for metabase
c1299a4
@matinnuhamunada
fix: pin gsl to 2.6 for mash
a23398f
@matinnuhamunada
chore: correct logging
014a38f
@matinnuhamunada
fix: correct zip location for BGC schema
49ab2e6
@matinnuhamunada
notebook: update np.matrix to np.asarray and fix eggnog
519e1aa
@matinnuhamunada
fix: rollback duckdb to version 38
f04e8ff
@matinnuhamunada
temporary_fix: use experimental dbt branch
f207901
@matinnuhamunada matinnuhamunada changed the title MIBIG update to 3.1 Updates and BGC Feature Jan 30, 2023
@matinnuhamunada matinnuhamunada merged commit b8afea6 into main Jan 30, 2023
@matinnuhamunada matinnuhamunada deleted the dev-0.6.0 branch March 4, 2023 18:35
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@OmkarSaMo OmkarSaMo Awaiting requested review from OmkarSaMo

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@matinnuhamunada matinnuhamunada

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MIBIG 3 on BiG-SCAPE
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@matinnuhamunada