Use PAQR and KAPAC

This repository provides all necessary information and scripts required to use the methods PAQR and/or KAPAC. Further down you find the link to a self-contained pipeline that runs both tools in combination.

To get you started, clone the repository and change to the directory you specified as target-directory:

git clone https://github.com/zavolanlab/PAQR_KAPAC.git path/to/workdir
cd path/to/workdir

Prepare the virtual environment

The execution of PAQR and KAPAC depends on specific software (like python, including several packages, or R). With the installation and activation of the virtual environment as it is shown below, you can ensure that both tools run properly.

Step 1: Download Miniconda3

On Linux:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

On MacOS X:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
bash Miniconda3-latest-MacOSX-x86_64.sh

Step 2: Creating a new python3 environment (with all required packages/software)

conda create -n paqr_kapac -c bioconda -c ostrokach --file requirements_py3.txt

If you already have a conda version with python2 installed, create the new python 3 environment like this:

conda create -n paqr_kapac -c bioconda -c ostrokach --file requirements_py3.txt python=3

With the installation of the environment, the following software is installed as well:

• Python (v3.5.1)
• Snakemake (v3.13.0)
• NumPy (v1.11.3)
• Graphviz (v2.38.0)
• PyYaml (v3.12)
• Docutils (v0.12)
• STAR (v2.5.2a)
• samtools (v1.3.1)
• bedtools (v2.26.0)
• gzip (v1.7)
• R (v3.3.2)
• SRA tools (v.2.8.2)

Step 3: Creating a new python2 environment to run PAQR

PAQR relies on packages that are available only for python2 currently. To ensure that PAQR runs properly, this python2 environment is installed.

conda create -n py2_paqr python=2 -c bioconda -c anaconda --file requirements_py2.txt

The following python packages are available in this python2 environment:

• HTSeq (v0.7.2)
• RseQC (v2.6.4)

Step 4: Activate the environment

(only the python3 environment needs to be activated; the py2_paqr environment is only used internally)

source activate paqr_kapac

To exit the environment (after finishing the usage of the pipeline), just execute

source deactivate