Python package to analyse ribosome profiling data. Most of the functionality has been ported to ribotricer
- Free software: BSD license
- Documentation: https://riboraptor.readthedocs.io/en/latest/
- 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 biocondaWe will create a searate environment inside conda for running riboraptor. The environment name is also riboraptor. If you already have a conda environment named riboraptor, you can delete it by running:
source deactivate riboraptor && conda env remove -n riboraptorWe will now install all the dependencies:
conda create --name riboraptor python=3 gcc matplotlib numpy pandas pybedtools \
pyBigWig pyfaidx pysam scipy seaborn statsmodels six click click-help-colors htseq biopython bx-python \
h5py joblib trackhub pytest snakemake sra-tools star fastqc trim-galore ucsc-bedgraphtobigwig ucsc-bedsort \
ucsc-bigwigmerge bamtools pysradb && source activate riboraptorWe also have the following two dependencies for processing and downloading SRA datasets:
- aspera connect : For allowing '.fasp' downloads from SRA
Linux download link: https://download.asperasoft.com/download/sw/connect/3.7.4/aspera-connect-3.7.4.147727-linux-64.tar.gz
- SRAdb : For fetching all experiments of a SRA project with the associated metadata
Since there is currently a bug in bioconductor-sradb, we will install it from github.
git clone https://github.com/seandavi/SRAdb
cd SRAdbRun R, and install SRAdb within R use devtools. Please make sure your riboraptor environment is already activated. (source activate riboraptor):
library(devtools)
devtools::install(".")And finally, we need two metadata files for processing SRA records:
mkdir riboraptor-data && cd riboraptor-data
wget -c http://starbuck1.s3.amazonaws.com/sradb/GEOmetadb.sqlite.gz && gunzip GEOmetadb.sqlite.gz
wget -c https://starbuck1.s3.amazonaws.com/sradb/SRAmetadb.sqlite.gz && gunzip SRAmetadb.sqlite.gzsource activate riboraptor
git clone https://github.com/saketkc/riboraptor.git
cd riboraptor
python setup.py install --single-version-externally-managed --record=record.txtWe will assume you have the following directory structure for the rest of our analysis:
| some_root_directory
| ├── riboraptor
| │ ├── snakemake
| │ └── setup.py
| ├── riboraptor-data
| │ ├── GEOmetadb.sqlite
| │ └── SRAmetadb.sqliteSee example workflow
See: https://riboraptor.readthedocs.io/en/latest/
In progress: http://ribopod.usc.edu/
See: https://riboraptor.readthedocs.io/en/latest/cmd-manual.html
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