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Python package to analyse ribosome profiling data

Project description

riboraptor : a pipeline for analysing ribosome profiling data

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Python package to analyse ribosome profiling data

Installation

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 git@github.com:saketkc/riboraptor.git
cd riboraptor
python setup.py 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 https://github.com/seandavi/SRAdb
cd SRAdb

Run R, and install SRAdb within R use devtools

library(devtools)
devtools::install(".")

History

0.2.0 (04-23-2018)

  • First release on PyPI.

Project details


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