BioInstaller package

Introduction

Conda and Bioconda have made us easy to install many packages and bio-softwares conveniently. Yet, learning how to install and compile bioinformatics softwares were still necessary. Because, the experience will help you to improve the ability of debugging.

Especialy, when start a NGS analysis work in a new computer or system, you need costs so much time and energy to establish a complete set of softwares and dependce of a analysis pipeline and set the corresponding configuration file.

BioInstaller can be used to download/install bioinformatics tools, dependences and databases in R relatively easily, and the information of installed softwares will be saved which can be used to generate configuration file. More detail can be founded in Document website.

Moreover, BioInstaller provide a different way to provide softwares download/install for others.

Installation

CRAN

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

Github

# Install the cutting edge development version from Lab-GitHub:
# Now only Jhuanglab members can get the source
# install.packages("devtools")
devtools::install_github("JhuangLab/BioInstaller")

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

Utils:

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

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