Installation

Dependencies

Core dependencies include:

  • Python3

  • The cgat-core pipeline framework

  • Python packages as per python/requirements.txt

  • R >= 4.0

  • Various R libraries (see R/install.packages.R)

  • The provided txseq R library

Installation

  1. Install the cgat-core pipeline system following the instructions here https://github.com/cgat-developers/cgat-core/.

  2. Clone and install the txseq repository e.g.

git clone https://github.com/sansomlab/txseq.git
cd txseq
python setup.py develop

Note

Running “python setup.py develop” is necessary to allow pipelines to be launched via the “txseq” command.

  1. In the same virtual or conda environment as cgat-core install the required python packages:

    pip install -r txseq/python/requirements.txt

  2. 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"))

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

    Rscript txseq/R/install.packages.R

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

    R CMD INSTALL R/txseq