Python modules

There are several extra python module requirements that are needed and are summarized in the following table:

Module	Version
biopython	1.78
future	0.18.2
HCGB	0.3.2
mirtop	0.4.23
multiqc	1.10
networkx	2.5
pybedtools	0.7.10
termcolor	1.1.0
numpy	1.18.4
pandas	0.24.2

These modules might have extra dependencies. Details of the list of all modules required are listed in XICRA/config/python/python_requirements.txt. And accessible here:

• Python requirements details

Although these dependencies will be fulfilled during the XICRA installation with pip, you might be interested in installing them yourself.

Using pip we can install them all at a glance.

pip install -r ./XICRA/config/python/python_requirements.txt

But again, following installation recommendations, we encourage you to create and install them within a virtual environment (See section: Python environment section for details).

You can test the presence of these python modules using the XICRA config module. Once you identified the missing dependencies and minimum versions required you can either install them and set them available within your PYTHONPATH or environment or you can execute the XICRA config with install option.

Software dependencies

Also, several software packages are also required. They are listed in XICRA/config/software/dependencies.csv, which is shown below:

software	version	export name	website
fastqc	0.11.4	fastqc	https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc
sRNAbench	1.6	sRNAbench.jar	https://bioinfo2.ugr.es/srnatoolbox/standalone/
optimir		optimir	https://github.com/FlorianThibord/OptimiR
miraligner		miraligner.jar	https://github.com/lpantano/seqbuster
STAR	2.6.1	STAR	https://github.com/alexdobin/STAR
featureCounts	1.5.1	featureCounts	http://subread.sourceforge.net/
fastqjoin		fastq-join	https://expressionanalysis.github.io/ea-utils/
cutadapt	2.10	cutadapt	https://cutadapt.readthedocs.io/en/stable/
multiqc	1.8	multiqc	https://multiqc.info/
miRTop	0.4.23	mirtop	https://github.com/miRTop/mirtop

Most of the software are common software that any person doing bioinformatics should have, so you might have already available within your system. However, installing XICRA using conda all the dependecies will be correctky installed.

You can test for any missing software dependencies using the XICRA config module. Once you identified the missing dependencies and minimum versions required you can either install them and set them available within your $PATH or you can execute the X config with install option.