Installation

Since v0.7, splicekit is a Snakemake pipeline with a Conda/micromamba environment.

# clone the repository
git clone git@github.com:bedapub/splicekit.git
cd splicekit

# create and activate the conda environment
micromamba create -y -f splicekit.yaml
micromamba activate splicekit

# install remaining (non-conda) dependencies: R/edgeR, Perl modules, jbrowse-cli
./install.sh

# install splicekit itself
pip install .

Note

install.sh installs R packages (edgeR via BiocManager), Perl SOAP/XML modules, and @jbrowse/cli via npm — these aren't packaged as conda dependencies, so run it once per environment.

The splicekit.yaml environment brings in Snakemake, STAR, samtools, subread (featureCounts), MEME (for DREME), rMATS and the snakemake-executor-plugin-cluster-generic plugin used for SLURM submission. See Dependencies for the full list.

Installing just the Python package

If you already have the environment's tools on your PATH (or are only using splicekit's Python API / running individual splicekit CLI steps by hand), you can install the package on its own:

pip install splicekit

or, from this repository directly:

pip install git+https://github.com/bedapub/splicekit.git@main

Note

On some systems, pip installs the executable scripts under ~/.local/bin. If this folder is not in your PATH, running splicekit will fail with command not found. Fix this with export PATH="$PATH:~/.local/bin" (add it to your ~/.profile to persist across logins). Another option is to install inside a virtual environment (using virtualenv).

Container

If you'd rather not install dependencies directly on the machine or cluster, set container = "singularity run docker://ghcr.io/bedapub/splicekit:main" in splicekit.config. splicekit will then run its non-Python steps through that imported Docker image (pybio and scanRBP are already installed as regular pip dependencies regardless of the container setting). See Configuration.