params <-
list(isSlides = "no")
## ----setup, include=FALSE-----------------------------------------------------
suppressPackageStartupMessages(require(knitr))
knitr::opts_chunk$set(echo = TRUE, tidy = T, eval=F)
## ---- results='asis',include=TRUE,echo=FALSE----------------------------------
if(params$isSlides != "yes"){
cat("# Conda
---
"
)
}
## ---- results='asis',include=TRUE,echo=FALSE----------------------------------
if(params$isSlides == "yes"){
cat("class: inverse, center, middle
# Herper
---
"
)
}else{
cat("# Herper
---
"
)
}
## -----------------------------------------------------------------------------
library(Herper)
install_CondaTools(tools = "star", env = "rnaseq")
## -----------------------------------------------------------------------------
my_miniconda <- "~/Desktop/My_Conda"
install_CondaTools(tools = "star", env = "rnaseq", pathToMiniConda = my_miniconda)
## -----------------------------------------------------------------------------
conda_paths <- install_CondaTools(tools = c("salmon","kallisto"), env = "rnaseq", updateEnv = TRUE , pathToMiniConda = my_miniconda)
conda_paths
## ----list_CondaPkgs-----------------------------------------------------------
list_CondaPkgs("rnaseq", pathToMiniConda = my_miniconda)
## ----conda_search-------------------------------------------------------------
conda_search("kall", pathToMiniConda = my_miniconda)
## ----conda_search22, eval=F, echo=F-------------------------------------------
## test <- capture.output(conda_search("salmon", pathToMiniConda = my_miniconda))
## write.csv(test,"../data/search_res.csv")
## ----conda_search2------------------------------------------------------------
conda_search("kallisto", pathToMiniConda = my_miniconda)
## ----conda_search_nuance------------------------------------------------------
conda_search("kallisto<=0.45", pathToMiniConda = my_miniconda)
## -----------------------------------------------------------------------------
conda_paths <- install_CondaTools(tools = "kallisto<=0.45", env = "rnaseq", updateEnv = T, pathToMiniConda = my_miniconda)
## -----------------------------------------------------------------------------
library(magrittr)
library(dplyr)
list_CondaPkgs("rnaseq", pathToMiniConda = my_miniconda) %>% dplyr::filter(name=="kallisto")
## ----with_condaenv_SalmonWithCondaEnvEval,echo=TRUE,eval=FALSE,tidy=FALSE-----
## res <- with_CondaEnv("rnaseq",
## system2(command="salmon",args = "help",stdout = TRUE),
## pathToMiniConda=my_miniconda)
## res
## ----with_condaenv_SalmonLocalCondaEnv,echo=TRUE,eval=FALSE-------------------
## salmonHelp<- function(){
## local_CondaEnv("rnaseq", pathToMiniConda=my_miniconda)
## helpMessage <- system2(command="salmon",args = "help",stdout = TRUE)
## helpMessage
## }
## salmonHelp()
## ----export-------------------------------------------------------------------
yml_name <- paste0("rnaseq_", format(Sys.Date(), "%Y%m%d"), ".yml")
export_CondaEnv("rnaseq", yml_name, pathToMiniConda = my_miniconda)
## -----------------------------------------------------------------------------
testYML <- system.file("extdata/test.yml", package="Herper")
import_CondaEnv(yml_import=testYML, pathToMiniConda = my_miniconda)
## ----import, eval=F, echo=F---------------------------------------------------
##
## is_windows <- function() {
## identical(.Platform$OS.type, "windows")
## }
## miniconda_conda <- function(path = miniconda_path()) {
## exe <- if (is_windows()) {
## "condabin/conda.bat"
## } else {
## "bin/conda"
## }
## file.path(path, exe)
## }
## pathToCondaInstall <- my_miniconda
## pathToConda <-miniconda_conda(pathToCondaInstall)
## pathToConda
## yml_import=testYML
## args <- paste0("-f", yml_import)
##
## result <- system2(pathToConda, shQuote(c("env", "create", "--quiet", "--json", args)), stdout = TRUE, stderr = TRUE)
## result
## ---- results='asis',include=TRUE,echo=FALSE----------------------------------
if(params$isSlides == "yes"){
cat("class: inverse, center, middle
# Pip
---
"
)
}else{
cat("# Pip
---
"
)
}
## -----------------------------------------------------------------------------
install_CondaTools("pip", "rnaseq", pathToMiniConda = my_miniconda, updateEnv = TRUE)
with_CondaEnv("rnaseq",
system2(command=paste0(conda_paths$pathToEnvBin,"/pip"),args = c("install", "scanpy"), stdout = TRUE),
pathToMiniConda=my_miniconda)
## -----------------------------------------------------------------------------
list_CondaPkgs("rnaseq", pathToMiniConda = my_miniconda) %>% dplyr::filter(name=="scanpy")