The Herper package is a simple toolset to install and manage Conda packages and environments from R.
The Herper package was developed by Matt Paul, Doug Barrows and Thomas Carroll at the Rockefeller University Bioinformatics Resources Center with contributions from Kathryn Rozen-Gagnon.
This Quick start gives a brief intro into getting up and running with Herper. Check the documentation website for more detailed information and use case examples.
Use the BiocManager package to download and install the
package from our Github repository:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Herper")Once installed, load it into your R session:
The install_CondaTools() function allows the user to specify required Conda software and the desired environment to install into.
Miniconda is installed as part of the process (by default into the r-reticulate’s default Conda location). If you already have Miniconda installed (or want to control the location of miniconda installation), you can specify the path with the pathToMiniConda parameter.
The install_CondaSysReqs checks the System Requirements for the specified R package, and uses Conda to install this software.
testPkg <- system.file("extdata/HerperTestPkg",package="Herper")
install.packages(testPkg,type = "source",repos = NULL)
condaDir <- file.path(tempdir(),"r-miniconda")
condaPaths <- install_CondaSysReqs("HerperTestPkg", pathToMiniConda = myMiniconda,SysReqsAsJSON=FALSE)
#' system2(file.path(condaPaths$pathToEnvBin,"samtools"),args = "--help")Thank you to Ji-Dung Luo and Wei Wang for testing/vignette review/critical feedback and Ziwei Liang for their support.
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
## [4] LC_COLLATE=C LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] Herper_1.17.0 reticulate_1.39.0 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] cli_3.6.3 knitr_1.48 rlang_1.1.4 xfun_0.48
## [5] png_0.1-8 jsonlite_1.8.9 rjson_0.2.23 buildtools_1.0.0
## [9] htmltools_0.5.8.1 maketools_1.3.1 sys_3.4.3 sass_0.4.9
## [13] rmarkdown_2.28 grid_4.4.1 evaluate_1.0.1 jquerylib_0.1.4
## [17] fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4 BiocManager_1.30.25
## [21] compiler_4.4.1 Rcpp_1.0.13 lattice_0.22-6 digest_0.6.37
## [25] R6_2.5.1 bslib_0.8.0 Matrix_1.7-1 withr_3.0.2
## [29] tools_4.4.1 cachem_1.1.0