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.

Feature:

  • More attention for those software and database resource that not be included in the other software warehouse
  • Extendible
  • Download 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

Contributed Resources

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 …

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 …

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