-
Notifications
You must be signed in to change notification settings - Fork 67
Installation
cziegenhain edited this page Nov 24, 2020
·
35 revisions
Note: zUMIs is only tested on typical Linux systems (eg Ubuntu, CentOS) and may not work on Windows, Windows Linux subsystem or MacOS.
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 zUMIsor use a Docker containing zUMIs!
- samtools >= 1.5 🔧 [tested: 1.7, 1.9, 1.10] Note: For non-UMI based methods, it is highly recommended to use samtools 1.7 and higher.
- STAR >= 2.5.4b 🌟 [RECOMMENDED: 2.5.4b or 2.7.X] Note: Some users have reported that some STAR versions (e.g. 2.6.0a) may produce problems when generating the reference index without GTF files.
- R >= 3.4 💻 [tested: 3.4.4, 3.5.2, 3.6.0, 4.0.2]
- pigz >= 2.3 🐷 [tested: 2.4]
To install R dependencies, please run the following:
cran_pcks <- c("inflection","yaml","shiny","shinythemes","shinyBS","ggplot2","mclust","dplyr","cowplot","Matrix","BiocManager","devtools","stringdist","data.table","stringr","extraDistr")
install.packages(cran_pcks)
bioc_pcks <- c("GenomicRanges","GenomicFeatures","GenomicAlignments","AnnotationDbi","GenomeInfoDb","plyranges")
BiocManager::install(bioc_pcks)
devtools::install_github('VPetukhov/ggrastr')
For faster demultiplexing of per-cell bam files, please have a valid installation of python3.x and the pysam (>=0.15) module.
For bioconductor version numbers, please check the sessionInfo() output of a validated zUMIs installation below:
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: elementary OS 5.1.6 Hera
Matrix products: default
BLAS: /home/chris/programs/R-4.0.2/lib/libRblas.so
LAPACK: /home/chris/programs/R-4.0.2/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=sv_SE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=sv_SE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=sv_SE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=sv_SE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] plyranges_1.8.0 AnnotationDbi_1.50.1
[3] GenomicAlignments_1.24.0 SummarizedExperiment_1.18.2
[5] DelayedArray_0.14.1 matrixStats_0.56.0
[7] Biobase_2.48.0 Rsamtools_2.4.0
[9] Biostrings_2.56.0 XVector_0.28.0
[11] GenomicRanges_1.40.0 GenomeInfoDb_1.24.2
[13] IRanges_2.22.2 S4Vectors_0.26.1
[15] BiocGenerics_0.34.0 extraDistr_1.8.11
[17] stringr_1.4.0 data.table_1.13.0
[19] stringdist_0.9.6 Matrix_1.2-18
[21] cowplot_1.0.0 dplyr_1.0.0
[23] mclust_5.4.6 ggplot2_3.3.2
[25] shinyBS_0.61 shinythemes_1.1.2
[27] shiny_1.5.0 yaml_2.2.1
[29] inflection_1.3.5
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 lattice_0.20-41 digest_0.6.25
[4] mime_0.9 R6_2.4.1 RSQLite_2.2.0
[7] pillar_1.4.6 zlibbioc_1.34.0 rlang_0.4.7
[10] blob_1.2.1 BiocParallel_1.22.0 RCurl_1.98-1.2
[13] bit_1.1-15.2 munsell_0.5.0 rtracklayer_1.48.0
[16] compiler_4.0.2 httpuv_1.5.4 pkgconfig_2.0.3
[19] htmltools_0.5.0 tidyselect_1.1.0 tibble_3.0.3
[22] GenomeInfoDbData_1.2.3 XML_3.99-0.5 crayon_1.3.4
[25] withr_2.2.0 later_1.1.0.1 bitops_1.0-6
[28] grid_4.0.2 xtable_1.8-4 gtable_0.3.0
[31] lifecycle_0.2.0 DBI_1.1.0 magrittr_1.5
[34] scales_1.1.1 stringi_1.4.6 promises_1.1.1
[37] ellipsis_0.3.1 generics_0.0.2 vctrs_0.3.2
[40] tools_4.0.2 bit64_0.9-7.1 glue_1.4.1
[43] purrr_0.3.4 fastmap_1.0.1 colorspace_1.4-1
[46] memoise_1.1.0