This package provides scripts and APIs in both python 3 and R. For running the level 0 processing steps (handling of fastq files), python 3 is required. For running DESeq2, R is required.
All code in this package has been tested on Python 3.6 - compatibility with newer and older versions has not been tested.
Python 3.6 support can be provided on Red Hat 7 systems by installing the following packages:
python36
python36-devel
python36-pip
Alternatively, an individual user can install Python 3 on Linux or Windows using Miniconda.
Once Python 3 and associated pip tool is installed, the following python libraries should be installed for the individual user:
pip3 install --user pandas pymongo mongoengineAll code in this package has been tested on R 3.6.0, but any version of R 3.x should be sufficient.
Package versions may have an impact due to changes in functionality or API.
The following R libraries are also required to use all features of the R code in Rlib/ directory:
- mongolite - Required for DB access in R, code has been tested with v2.1.0.
- jsonlite - Required for DB access and handling JSON files, code has been tested with v1.6.
- reldist - Required for computing Gini coefficients when applying QC checks on Level 1 count data, code has been tested with v1.6-6.
- DESeq2 - Required for differential expression analysis, code has been tested and all published analysis run with v1.24.0.
Currently, it is recommended to clone the entire repository to a user or analysis directory by running:
git clone https://github.com/USEPA/httrpl_pilot.git (/path/to/analysis)To confirm that all requirements have been successfully installed, run the following command:
python3 (localpath)/httrpl/bin/testInstall.pyExecutable scripts are in: bin/
Python modules are in: lib/
R modules are in: Rlib/
- Logan J. Everett
- Imran Shah
- Joseph Bundy
- Derik Haggard
- Beena Vallanat