Installation

Install through docker (recommended)

exSEEK requires a lot of other tools to run. To save efforts for environment setup, you can use our prepared docker image:
To get more information about docker, you can visit the official site of docker.

After installing docker, you can download the image through the following command:

docker pull ltbyshi/exseek

Then you can invoke the main script exseek from docker:

docker run --rm -it -v $PWD:/workspace -w /workspace ltbyshi/exseek exseek.py "$@"

This will mount the current directory to /workspace as root directory of input and output files. You can also replace $PWD with another directory

Alternatively, you can use use singularity or udocker to run the container for Linux kernel < 3 or if you don't have permission to use docker.

Install through singularity

First install singularity according to (https://singularity.lbl.gov/install-linux).

Then build a singularity image from docker:

mkdir -p singularity
singularity build singularity/exseek.simg docker://ltbyshi/exseek

Finally you need to change the variable container.image to the path of the singularity image in the configuration file.

To run a pipeline through udocker, you can add --runner singularity option to theexseek` command.

Install through udocker

First install udocker according to (https://github.com/indigo-dc/udocker/blob/master/doc/installation_manual.md).

Then download the docker image using udocker:

udocker pull ltbyshi/exseek
udocker create --name=exseek ltbyshi/exseek

Finally you need to change the variable container.image to the path of the name of the udocker image in the configuration file.

To run a pipeline through udocker, you can add --runner udocker option to the exseek command.

Manual installation

Install required software

Before running exSEEK, you need to install the following software. It is recommended to install most of the software through conda
with the bioconda channel and conda-forge channel appended.

You can refer to the Dockerfile for commands to install the dependencies. You should also ensure that the executables are added to the $PATH environment variable.

Software	Version	Description
Python	3.6	Python interpreter
R	3.5.3	R interpreter
Java		Java runtime support
pandas		Python package for dataframe operations.
matplotlib		Python package for plotting.
seaborn		Python package for high-level plotting.
h5py		Python package for matrix storage.
scikit-learn		Python package for machine learning
mlextend		Python package for extra machine learning algorithms compatible with scikit-learn
skrebate		Python package for feature selection compatible with scikit-learn
flask		Python package for building lightweight web apps
jinja2		Python package for template rendering
umap		Python package for dimensional reduction using UMAP
snakemake		Python package for pipeline building
tqdm		Python package for progress monitoring
bedtools		Tools for operation of BED files.
samtools		Tools for operation of SAM/BAM files.
STAR		RNA mapping software.
bowtie2		RNA mapping software.
subread		Read counting (featureCounts)
RSEM		Gene quantification
bamtools		Tools for operation of BAM files.
cutadapt		Versatile tool for adapter trimming.
picard		Tools for operation of SAM/BAM files.
gffread		Tool for conversion between GTF/GFF and other formats.
gffcompare		Tool for merging GTF/GFF files.
bedToGenePred		Convert BED file to GenePred format
genePredToGtf		Convert genePred file to GTF format
bedGraphToBigWig		Convert bedGraph file to BigWig format
bigWigToBedGraph		Convert BigWig file to BedGraph format
HT-seq		Read counting
FastX Toolkit		Tools for operation of FASTQ/FASTA files
BioPython		Python package for reading/writing various file formats used in bioinformatics
MultiQC		Python package for generating graphical reports for quality control results
pigz		Parallel version of gzip

Install exSEEK

The next command installs exSEEK as a Python package, with a main script named exseek added to PATH:

python setup.py install

After installation, you can test by running:

exseek --help