biocomposer
Graph-based orchestration of bioinformatics tools. Full documentation: https://mlberkeley.github.io/BioComposer-graph-based-orchestration-of-bioinformatics-tools-documentation/
Setup (both local and Modal)
pip install biocomposer
mkdir inputs # put your FASTA/PDB/etc. files here
mkdir run # holds your pipeline script
Create a .env file in your working directory with the API key(s) you use
(GEMINI_API_KEY, GOOGLE_API_KEY, ANTHROPIC_API_KEY, or OPENAI_API_KEY).
Create run/run_pipeline.py to define your pipeline.
Running locally
Prerequisites: Docker installed and running, bv installed (cargo install biov).
biocomp run run/run_pipeline.py --env .env
Outputs go to ./results/.
Running on Modal
pip install modal
modal setup
biocomp run --modal run/run_pipeline.py --env .env
modal volume get biocomp results/fasttree_output_1/stdout/fasttree_stdout.txt ./fasttree_stdout.txt
Flags
--env <path> [both] env file with API keys (default .env)
--clean [both] clear previous outputs first
--modal [both] run on Modal instead of locally
--gpu T4 [modal] GPU type (default A10G)
--memory 32768 [modal] sandbox memory in MB (default 8192)
--shell [modal] drop into an interactive sandbox shell
Overriding a tool's command
By default a node runs the tool's entrypoint binary with its registry args.
Override either when needed (slots like {input}/{output} map to the node's I/O):
# run a different exposed binary instead of the entrypoint
g.add_node("trimal", entrypoint_override="readal")
# replace the argument template
g.add_node("colabfold", args_override="--num-recycle 0 {fasta} {output_dir}")
# both together (common for non-entrypoint binaries)
g.add_node("trimal", entrypoint_override="readal",
args_override="-in {alignment} -out {trimmed} -fasta")
1 maintainer
Metadata
1 maintainer
Release files for biocomposer 0.1.4
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Release files / biocomposer-0.1.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
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