Installation

NOTES: Only python2 is supported

Prerequisites

Softwares:
- bwa
- hisat2
- stringtie
- samtools >= 1.9 (*older version of samtools may use deprecated parameters in `sort` and `index` commands*)

Python packages:
- PyYAML
- argparse
- pysam
- numpy
- scipy
- scikit-learn

Use the released version (Recommended)

Download the latest released version of CIRIquant from GitHub

The released package is a packed conda environment including all dependencie, make sure you have installed anaconda in your environment

# Download packed package
wget https://github.com/bioinfo-biols/CIRIquant/releases/download/v1.1.3/CIRIquant_v1.1.3.tar.gz
mkdir -p CIRIquant_env
tar zxvf CIRIquant_v1.1.3.tar.gz -C CIRIquant_env

# Configuration environments (required)
conda activate ./CIRIquant_env
cd CIRIquant_env
make

Activate CIRIquant environment and test

conda activate /path/to/CIRIquant_env
which CIRIquant

Install CIRIquant and dependencies using conda (Not recommended)

Save the following content to a file called environment.yml:

name: CIRI
channels:
- defaults
- bioconda
- conda-forge
dependencies:
- bioconda::bwa=0.7.17
- bioconda::hisat2=2.2.0
- bioconda::stringtie=2.1.1
- bioconda::samtools>=1.10
- bioconda::bioconductor-edger=3.28.0
- bioconda::bioconductor-limma=3.42.0
- conda-forge::r-statmod=1.4.35
- conda-forge::r-base=3.6
- conda-forge::r-optparse=1.6.6
- python=2.7.15
- pip=20.0.2
- perl=5.26.2
- pip:
  - CIRIquant>=1.1.2
  - numexpr==2.6.9
  - numpy==1.16.4
  - pysam==0.15.2
  - PyYAML==5.4
  - scikit-learn==0.20.3
  - scipy==1.2.2
  - argparse>=1.2.1

After you have saved the file just run:

# this installs the dependencies specified in the yml file
conda env create -f environment.yml
# this activates the conda environment
conda activate CIRI

# this will return the path bwa, hisat2, stringtie or samtools are installed to
# these paths need to be specified in the CIRI configuration file when running the tool
which bwa
which hisat2
which stringtie
which samtools

Install CIRIquant using pip

pip install CIRIquant

Install CIRIquant from source code

Use the setup.py for CIRIquant installation (clean install using virutalenv is highly recommended).

# create and activate virtual env
pip install virtualenv
virtualenv -p /path/to/your/python2/executable venv
source ./venv/bin/activate

# Install CIRIquant and its requirement automatically
tar zxvf CIRIquant.tar.gz
cd CIRIquant
python setup.py install

# Manual installation of required pacakges is also supported
pip install -r requirements.txt

The package should take approximately 40 seconds to install on a normal computer.