riboraptor 0.2.2

Python package to analyse ribosome profiling data

riboraptor : a pipeline for analysing ribosome profiling data

Python package to analyse ribosome profiling data

• Free software: BSD license

• Documentation: http://saketkc.github.io/riboraptor/

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 [e-mail]: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(".")

Features

See: http://saketkc.github.io/riboraptor/cmd-manual.html

History

0.2.0 (04-23-2018)

• First release on PyPI.