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Python package to analyse ribosome profiling data

Project description

riboraptor : a pipeline for analysing ribosome profiling data

Python package to analyse ribosome profiling data


Setting up conda

  1. Install conda, the best way to install it is with the Miniconda package.The Python 3 version is recommended.
  2. Set up channels, It is important to add them in this order.
conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

Installing dependencies

conda create --name riboraptor python=3.6 matplotlib numpy pandas pybedtools \
pyBigWig pyfaidx pysam scipy seaborn statsmodels six click click-help-colors htseq biopython \
snakemake sra-tools star fastqc trim-galore ucsc-bedgraphtobigwig ucsc-bedsort

Installing riboraptor

source activate riboraptor
git clone
cd riboraptor
python install --single-version-externally-managed --record=/tmp/record.txt

Downloading datasets from SRA

  1. Install aspera connect
  2. Install additional dependencies
source activate riboraptor
conda install gcc
conda install -c r r=3.4.1
conda install -c bioconda bioconductor-annotationdbi bioconductor-geometadb
conda install -c r r-devtools

Since there is currently bug with bioconductor-sradb, we will install it from github

git clone
cd SRAdb

Run R, and install SRAdb within R use devtools



0.2.0 (04-23-2018)

  • First release on PyPI.

Project details

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