diff --git a/README.md b/README.md index cc8dbba..1026f4b 100644 --- a/README.md +++ b/README.md @@ -65,6 +65,24 @@ Details on the models are provided in the respective subfolders as well as in th Here, we provide a brief description on the core funtionality of TEPIC, the computation of TF-gene scores. ## Installing TEPIC + +### Using conda + +If you use conda, create the required environment by running + + conda env create tepic -f conda.yaml + +Activate the environment using + + conda activate tepic + +Then, in the Code/ directory, compile TRAPmulti.cpp + + g++ TRAPmulti.cpp -O3 -fopenmp -o TRAPmulti + +You can now use TEPIC.sh + +### Manual installation To run *TEPIC* the following packages/software must be installed: * Python (minimum version 2.7) * [bedtools](https://github.com/arq5x/bedtools2): Installation instructions for bedtools can be found [here](http://bedtools.readthedocs.io/en/latest/content/installation.html). Please make sure to add diff --git a/conda.yaml b/conda.yaml new file mode 100644 index 0000000..6baa1a3 --- /dev/null +++ b/conda.yaml @@ -0,0 +1,18 @@ +name: TEPIC +channels: + - bioconda + - conda-forge + - r +dependencies: + - compilers + - bedtools + - numpy + - scipy + - twobitreader + - r-gplots + - r-ggplot2 + - r-glmnet + - r-domc + - r-reshape2 + - r-gridextra + - r-data.table