Installation¶

Install the pipeline¶

Install R dependencies¶

The TXSeq pipeline requires R>=4.5 and the optparse tximeta and tximport packages.

Install the Python dependencies¶

module purge 
unset PYTHONPATH
# Create a python virtual environment Ideally with uv on it 
uv venv txseq_venv --python 3.14
source ./txseq_venv/bin/activate
cd txseq_venv
git clone https://github.com/sansomlab/txseq_snakemake.git
cd txseq_venv
uv pip install -e .

To install the TXSeq R package¶

Make sure you have the “devtools” and “BiocManager” R libraries pre-installed by running the following command in an R shell:

install.packages(c("devtools","BiocManager"))

Install the required R packages by running the following command from the bash shell:

Rscript src/txseq/R/txseq/install.packages.R

Install the txseq R library by running the following command from the bash shell:

R CMD INSTALL src/txseq/R/txseq