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dvc.yaml
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stages:
dependencies:
cmd: bash src/0_dependencies.sh
toxvaldb:
cmd: Rscript src/01_integrate_toxvaldb.R
deps:
- src/01_integrate_toxvaldb.R
outs:
[staging/toxvaldb: {cache: false}]
chembl:
cmd: Rscript src/02_integrate_chembl.R
deps:
- src/02_integrate_chembl.R
outs:
- staging/chembl
tox21:
cmd: Rscript src/03_integrate_tox21.R
deps:
- src/03_integrate_tox21.R
outs:
- staging/tox21
toxcast:
cmd: Rscript src/04_integrate_toxcast.R
deps:
- src/04_integrate_toxcast.R
outs:
- staging/toxcast
reach:
cmd: Rscript src/05_integrate_reach.R
deps:
- src/05_integrate_reach.R
outs:
- staging/reach
ice:
cmd: Rscript src/06_integrate_ice.R
deps:
- src/06_integrate_ice.R
outs:
- staging/ice
ctdbase:
cmd: Rscript src/07_integrate_ctdbase.R
deps:
- src/07_integrate_ctdbase.R
outs:
- staging/ctdbase
pubchem:
cmd: python3 src/09_integrate_pubchem.py
deps:
- src/09_integrate_pubchem.py
outs:
[staging/pubchem: {cache: false}]
toxrefdb:
cmd: Rscript src/11_integrate_toxrefdb.R
deps:
- src/11_integrate_toxrefdb.R
outs:
- staging/toxrefdb
# qsartoolbox:
# cmd: Rscript src/09_integrate_qsartoolbox.R
# deps:
# - src/09_integrate_qsartoolbox.R
# outs:
# - staging/qsartoolbox
bindingdb:
cmd: Rscript src/10_integrate_bindingdb.R
deps:
- src/10_integrate_bindingdb.R
outs:
- staging/bindingdb
BBBP:
cmd: python src/13_integrate_BBBP.py
deps:
- src/13_integrate_BBBP.py
outs:
- staging/BBBP
BACE:
cmd: python src/14_integrate_BACE.py
deps:
- src/14_integrate_BACE.py
outs:
- staging/BACE
sider:
cmd: python src/15_integrate_sider.py
deps:
- src/15_integrate_sider.py
outs:
- staging/sider
clintox:
cmd: python src/16_integrate_clintox.py
deps:
- src/16_integrate_clintox.py
outs:
- staging/CLINTOX
tox21_12:
cmd: python src/17_integrate_tox21_12.py
deps:
- src/17_integrate_tox21_12.py
outs:
- staging/Tox21
harmonize:
cmd: env/bin/python src/80_harmonize.py
deps:
- staging/bindingdb
- staging/chembl
- staging/ctdbase
- staging/ice
- staging/pubchem
- staging/reach
- staging/tox21
- staging/toxcast
- staging/toxrefdb
- staging/toxvaldb
- staging/BBBP
- staging/BACE
- staging/sider
- staging/CLINTOX
- staging/Tox21
- src/80_harmonize.py
outs:
- brick/substances.parquet
- brick/properties.parquet
- brick/activities.parquet
build_property_categories:
cmd: python src/91_property_categories.py
deps:
- brick/properties.parquet
- src/91_property_categories.py
outs:
- joblib_cache/assign_categories:
persist: true
- brick/property_categories.parquet:
persist: true
build_property_titles:
cmd: python src/92_llm_property_titles.py
deps:
- brick/properties.parquet
- brick/property_categories.parquet
- src/92_llm_property_titles.py
outs:
- joblib_cache/assign_titles:
persist: true
- brick/property_titles.parquet:
persist: true