Installation¶

pip install insilico-cancer-center

Graph drawing uses pygraphviz, which needs the system Graphviz library installed first (e.g. brew install graphviz, apt-get install graphviz graphviz-dev, or conda install -c conda-forge graphviz).

From source¶

git clone https://github.com/pedrofale/iscc
cd iscc
poetry install

Non-Python dependencies¶

Growth, sampling and the DNA/RNA/spatial assays need nothing beyond the Python stack. Two features shell out to external binaries, which iscc finds on $PATH:

Feature	Needs
Graph drawing (`pygraphviz`)	`graphviz`
FASTQ emission (`emit_dna_reads`)	`dwgsim` (program version ≥ 0.1.13) or `art_illumina`
BAM alignment (`emit_dna_reads(emit_bam=True)`)	`bwa` + `samtools`

environment.yml in the repository root declares them all:

conda env create -f environment.yml

Then poetry install into that environment for the Python packages. Without these binaries the read emitter still builds the reference, the per-cell FASTA, the coverage budget and the exact simulator command — it returns status="skipped:<tool>" instead of writing FASTQ, so the rest of the pipeline is unaffected.

Command-line tools¶

Installing the package provides the pipeline entry points:

Tool	Stage
`isccsim`	grow a tumor
`isccsample`	biopsy / dissociate into a sample
`isccdata`	generate DNA/RNA/spatial assay data
`isccfig`, `isccgif`	figures and animations

Once installed, see the Overview for the pipeline and a quickstart.