============================================================= riboraptor : a pipeline for analysing ribosome profiling data

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.. _Miniconda: https://conda.io/miniconda.html .. _aspera connect: http://downloads.asperasoft.com/connect2/ .. _Line4 snakemake/jobscript.sh: https://github.com/saketkc/riboraptor/blob/47c8a50753c2bcc96b57d43b525a47bb8fde2d04/snakemake/jobscript.sh#L4 .. _Line6 snakemake/cluster.yaml: https://github.com/saketkc/riboraptor/blob/47c8a50753c2bcc96b57d43b525a47bb8fde2d04/snakemake/cluster.yaml#L6 .. _Line7 snakemake/cluster.yaml: https://github.com/saketkc/riboraptor/blob/47c8a50753c2bcc96b57d43b525a47bb8fde2d04/snakemake/cluster.yaml#L7 .. _SRAdb: https://www.bioconductor.org/packages/3.7/bioc/html/SRAdb.html .. _GSE37744: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37744 .. _example workflow: ./docs/example_workflow.rst

Python package to analyse ribosome profiling data. Most of the functionality has been ported to ribotricer <https://github.com/smithlabcode/ribotricer>_

• Free software: BSD license
• Documentation: https://riboraptor.readthedocs.io/en/latest/

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**.

.. code-block:: bash

   conda config --add channels r
   conda config --add channels defaults
   conda config --add channels conda-forge
   conda config --add channels bioconda


Installing dependencies

We 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:

.. code-block:: bash

source deactivate riboraptor && conda env remove -n riboraptor

We will now install all the dependencies:

.. code-block:: bash

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 riboraptor

We 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.

.. code-block:: bash

git clone https://github.com/seandavi/SRAdb cd SRAdb

Run R, and install SRAdb within R use devtools. Please make sure your riboraptor environment is already activated. (source activate riboraptor):

.. code-block:: r

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

And finally, we need two metadata files for processing SRA records:

.. code-block:: bash

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.gz

Installing riboraptor

.. code-block:: bash

   source activate riboraptor
   git clone https://github.com/saketkc/riboraptor.git
   cd riboraptor
   python setup.py install --single-version-externally-managed --record=record.txt

We 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.sqlite


Using riboraptor
----------------

Usage mode 1: use riboraptor as a Snakemake based workflow

See example workflow_

Usage mode 2: use riboraptor as a standalone toolkit

See: https://riboraptor.readthedocs.io/en/latest/
  

Usage mode 3: ribopod - database
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In progress: http://ribopod.usc.edu/


Features
--------

See: https://riboraptor.readthedocs.io/en/latest/cmd-manual.html