Installation

Install zUMIs

zUMIs is a command line tool written in perl, shell and R. zUMIs can be installed by installing the dependencies and cloning the repository as given below.

git clone https://github.com/sdparekh/zUMIs.git

Alternatively, you can start your own Amazon cloud instance with a preinstalled copy of zUMIs!

Dependencies

General

• samtools >= 1.1 🔧
• STAR >= 2.5.3a 🌟
• R >= 3.4 💻
• pigz >= 2.3 🐷

R

To install R dependencies, please run the following:

ipak <- function(pkg, repository = c("CRAN", "Bioconductor", "github")) {
    new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
    if (length(new.pkg)) {
        if (repository == "CRAN") {
            install.packages(new.pkg, dependencies = TRUE)
        }
        if (repository == "Bioconductor") {
            source("https://bioconductor.org/biocLite.R")
            biocLite(new.pkg, dependencies = TRUE, ask = FALSE)
        }
        if (repository == "github") {
            devtools::install_github(pkg, build_vignettes = FALSE)
        }
    }
}

#CRAN packages
cranpackages <- c("dplyr","tidyr","devtools","reshape2","data.table","optparse","cowplot","mclust","Matrix")
ipak(cranpackages, repository = "CRAN")

# BIOCONDUCTOR packages
biocpackages <- c("AnnotationDbi","GenomicRanges","GenomicFeatures","GenomicAlignments")
ipak(biocpackages, repository = "Bioconductor")

#zUMIs requires Rsubread 1.26.0
install.packages("https://bioarchive.galaxyproject.org/Rsubread_1.26.0.tar.gz", repos = NULL, type = "source")

# GITHUB packages
githubpackages <- c("hadley/multidplyr")
ipak(githubpackages, repository = "github")

For bioconductor version numbers, please check the sessionInfo() output of a working zUMIs installation below:

>sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] tibble_1.3.3               cowplot_0.7.0             
 [3] ggplot2_2.2.1              GenomicAlignments_1.12.1  
 [5] Rsamtools_1.28.0           Biostrings_2.44.0         
 [7] XVector_0.16.0             SummarizedExperiment_1.6.1
 [9] DelayedArray_0.2.2         matrixStats_0.52.2        
[11] GenomicFeatures_1.28.0     AnnotationDbi_1.38.0      
[13] Biobase_2.36.2             GenomicRanges_1.28.2      
[15] GenomeInfoDb_1.12.0        IRanges_2.10.1            
[17] S4Vectors_0.14.1           BiocGenerics_0.22.0       
[19] Rsubread_1.26.0            data.table_1.10.5         
[21] reshape2_1.4.2             tidyr_0.6.3               
[23] dplyr_0.5.0                multidplyr_0.0.0.9000     
[25] optparse_1.3.2            

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11            compiler_3.4.1          plyr_1.8.4             
 [4] bitops_1.0-6            tools_3.4.1             zlibbioc_1.22.0        
 [7] biomaRt_2.32.0          digest_0.6.12           memoise_1.1.0          
[10] RSQLite_1.1-2           gtable_0.2.0            lattice_0.20-35        
[13] rlang_0.1.1             Matrix_1.2-10           DBI_0.6-1              
[16] GenomeInfoDbData_0.99.0 rtracklayer_1.36.0      stringr_1.2.0          
[19] grid_3.4.1              getopt_1.20.0           R6_2.2.2               
[22] BiocParallel_1.10.1     XML_3.98-1.7            magrittr_1.5           
[25] scales_0.4.1            assertthat_0.2.0        colorspace_1.3-2       
[28] stringi_1.1.5           RCurl_1.95-4.8          lazyeval_0.2.0         
[31] munsell_0.4.3