Set up - JGEnglishLab/TRE-MPRA-Pipeline GitHub Wiki
Set Up
Required Dependencies
TMP has a few dependencies required to run. If you do not want to download these software, we highly recommend using the docker image we've created that will include all of the needed dependencies. Follow the link to this github for instructions on how to download and run the docker image.
- Miniconda
- Miniconda will be used to download Starcode, Trim-Galore, and Snakemake
- (See set up section for more details on setting up a conda environment)
- Starcode (starcode-v1.4 2021-09-22)
- Trim-galore (version 0.6.10)
- ea-utils
- Once it has been downloaded and built (see additional instructions)you must add it to your path.
- Here are some instructions on how to add something to your path if you are unfamiliar.
- R
- R will require the following packages
- tidyverse
- dplyr
- testit
- png
- ggplot
- stringr
- BiocParallel
- MPRAnalyze
- R will require the following packages
- Python 3.9.7
- Python will require the following packages
- numpy
- pandas
- biopython
- Python will require the following packages
Set Up
- General
- Clone the repository into the desired location
- In the cloned repo go to the /barcode_map_data directory and unzip the finalBarcodeMap.csv.zip file
- Setting up a conda environment
- Set up a new environment
conda create -y -n tmp_env - Activate your new environment
conda activate tmp_env - Run the following commands
conda install python=3.9.7conda install -c bioconda trim-galoreconda install -c bioconda starcodeconda install -c bioconda snakemake
- Set up a new environment