Dependencies

Conda/micromamba environment (splicekit.yaml)

Installed by micromamba create -y -f splicekit.yaml:

pigz, deeptools, samtools, Snakemake, R (r-base, r-locfit), STAR, rMATS, Node.js, Ghostscript, subread (featureCounts, > 2.0.6), MEME (> 5.5.1, for DREME), Perl's cpanminus, and the snakemake-executor-plugin-cluster-generic pip package (used by run_snakemake_slurm.sh for SLURM submission).

Installed by install.sh

• R packages: BiocManager, data.table, statmod, R.utils, and Bioconductor's edgeR.
• Perl modules for the JBrowse2/SOAP tooling (XML::Compile::*, Log::Log4perl, Math::CDF, JSON, and others).
• @jbrowse/cli via npm install -g, used to set up the local JBrowse2 instance.

Python dependencies (installed by pip install .)

Levenshtein, logomaker, plotly, python-dateutil, pybio, scanRBP, pysam, numpy, psutil, beautifulsoup4, requests and rangehttpserver.

Optional

Singularity — only needed if you set container = "singularity run docker://ghcr.io/bedapub/splicekit:main" in splicekit.config instead of installing the conda environment directly. See Installation: Container.