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
- Install conda, the best way to install it is with the Miniconda package.The Python 3 version is recommended.
- 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
- Install aspera connect
- 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(".")