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
#You can install this package directly from CRAN by running (from within R):
install.packages('BioInstaller')# install.packages("devtools")
devtools::install_github("JhuangLab/BioInstaller")- GitHub resource
- GitHub resource meta information
- Non GitHub resource
- Non Github resource meta infrmation
- Database
- Web Service
- Docker
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 …
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 RPlease 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.
R package:
Related Other Resources
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License