BioInstaller package

Introduction

BioInstaller is a downloader and installer of bio-software and bio-databases. The inspiration for this project comes from the various types package manager, such as pip for Python package, install.packages for R package, biocLite for Bioconductor R package, etc.

Why we do not have an integrated bioinformatics database and software package manager?

In fact, there are already some tools can complete part of the work:

Conda and BioConda have done a lot of work and we can use them to conveniently install some of the bioinformatics software. But there are still many problems with these package managers, such as version updating not timely, incompatible to some pre-compiled programs, little support for the database and other non-software files.

docker is another kind very promising tool to complete the migration of the analytical environment. But the root authority is required that it’s difficult for you to always get root privileges.

Furthermore, learning how to install and compile bioinformatics software is still necessary, because these ‘unpleasant’ experience will help you to improve the ability to debug and modify programs.

As for me, when starting some NGS analysis work on a new computer or operating system, I have to spend much time and energy to establish a complete set of software and dependent files and set the corresponding configuration file.

BioInstaller can help us to download, install and manage a variety of bioinformatics tools and databases more easily and systematically.

What’s more, BioInstaller provides a different way to download and install your files, software, and databases for others, more detail can be found in another vignette Examples of Templet Configuration File.

A simple guide can be found in here.

Feature:

• More attention for those software and database resource that not be included in the other software warehouse
• Extendible
• Craw the source code and version information from the original site
• One step installation or download software and databases (Partial dependence supported)
• A software and database resources pool

Installation

CRAN

#You can install this package directly from CRAN by running (from within R):
install.packages('BioInstaller')

Github

# install.packages("devtools")
devtools::install_github("JhuangLab/BioInstaller")

Contributed Resources

• GitHub resource
• GitHub resource meta information
• Non GitHub resource
• Non Github resource meta infrmation
• Database
• Web Service
• Docker

Support Summary

Quality Control:

• FastQC, PRINSEQ, SolexaQA, FASTX-Toolkit

Alignment and Assembly:

• BWA, STAR, TMAP, Bowtie, Bowtie2, tophat2, hisat2, GMAP-GSNAP, ABySS, SSAHA2, Velvet, Edean, Trinity, oases, RUM, MapSplice2, NovoAlign

Variant Detection:

• GATK, Mutect, VarScan2, FreeBayes, LoFreq, TVC, SomaticSniper, Pindel, Delly, BreakDancer, FusionCatcher, Genome STRiP, CNVnator, CNVkit, SpeedSeq

Variant Annotation:

• ANNOVAR, SnpEff, VEP, oncotator

Utils:

• htslib, samtools, bcftools, bedtools, bamtools, vcftools, sratools, picard, HTSeq, seqtk, UCSC Utils(blat, liftOver), bamUtil, jvarkit, bcl2fastq2, fastq_tools

Genome:

• hisat2_reffa, ucsc_reffa, ensemble_reffa

CHIP-seq Analysis:

• MACS, CEAS

Others:

• sparsehash, SQLite, pigz, lzo, lzop, bzip2, zlib, armadillo, pxz, ROOT, curl, xz, pcre, R, gatk_bundle, ImageJ, igraph

Databases:

• ANNOVAR, blast, CSCD, GATK_Bundle, biosystems, civic, denovo_db, dgidb, diseaseenhancer, drugbank, ecodrug, expression_atlas, funcoup, gtex, hpo, inbiomap, interpro, medreaders, mndr, msdd, omim, pancanqtl, proteinatlas, remap2, rsnp3, seecancer, srnanalyzer, superdrug2, tumorfusions, varcards

Docker

You can use the BioInstaller in Docker since v0.3.0.

docker pull bioinstaller/bioinstaller:develop
docker run -it -v /tmp/download:/tmp/download bioinstaller/bioinstaller:develop R

How to contribute?

Please fork the GitHub BioInstaller repository, modify it, and submit a pull request to us. Especialy, the files list in contributed section should be modified when you see a tool or database that not be included in the other software warehouse.

Maintainer

Jianfeng Li

License

R package:

MIT

Related Other Resources

Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License