From 899c852296fb4dd1dc602d0afec34b3f6fd389da Mon Sep 17 00:00:00 2001 From: bschilder Date: Fri, 1 Sep 2023 17:09:56 +0100 Subject: [PATCH 1/8] Add rworkflows --- .Rbuildignore | 2 ++ .github/workflows/rworkflows.yml | 57 ++++++++++++++++++++++++++++++++ .gitignore | 1 + README.md | 2 +- 4 files changed, 61 insertions(+), 1 deletion(-) create mode 100644 .Rbuildignore create mode 100644 .github/workflows/rworkflows.yml diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 00000000..91114bf2 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,2 @@ +^.*\.Rproj$ +^\.Rproj\.user$ diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml new file mode 100644 index 00000000..34df233c --- /dev/null +++ b/.github/workflows/rworkflows.yml @@ -0,0 +1,57 @@ +name: rworkflows +'on': + push: + branches: + - master + - main + - devel + - RELEASE_** + pull_request: + branches: + - master + - main + - devel + - RELEASE_** +jobs: + rworkflows: + permissions: + contents: write + runs-on: ${{ matrix.config.os }} + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + container: ${{ matrix.config.cont }} + strategy: + fail-fast: ${{ false }} + matrix: + config: + - os: ubuntu-latest + bioc: devel + r: auto + cont: bioconductor/bioconductor_docker:devel + rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release + - os: macOS-latest + bioc: release + r: auto + cont: ~ + rspm: ~ + - os: windows-latest + bioc: release + r: auto + cont: ~ + rspm: ~ + steps: + - uses: neurogenomics/rworkflows@master + with: + run_bioccheck: ${{ false }} + run_rcmdcheck: ${{ true }} + as_cran: ${{ true }} + run_vignettes: ${{ true }} + has_testthat: ${{ true }} + run_covr: ${{ true }} + run_pkgdown: ${{ true }} + has_runit: ${{ false }} + has_latex: ${{ false }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run_docker: ${{ false }} + DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} + runner_os: ${{ runner.os }} + cache_version: cache-v1 diff --git a/.gitignore b/.gitignore index 65d29924..0420c714 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ .DS_Store .DS_Store +.Rproj.user diff --git a/README.md b/README.md index 0fee95a7..0452f8f3 100755 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@

- +[![rworkflows](https://github.com/GreenleafLab/ArchR/workflows/rworkflows/badge.svg)](https://github.com/GreenleafLab/ArchR/actions) [![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) ### ArchR has new features available for scATAC-seq Analysis From 04823e5680ae2db8b29224bef9c6b783f2ddd805 Mon Sep 17 00:00:00 2001 From: bschilder Date: Fri, 1 Sep 2023 17:10:47 +0100 Subject: [PATCH 2/8] Add rworkflows --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index 0420c714..0a295973 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ .DS_Store .DS_Store .Rproj.user +.Rhistory +.RData \ No newline at end of file From 94cd80512da5bc605ff40db2f442064376f94530 Mon Sep 17 00:00:00 2001 From: bschilder Date: Fri, 1 Sep 2023 17:11:35 +0100 Subject: [PATCH 3/8] fix badges [skip ci] --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 0452f8f3..f2cb1898 100755 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@

-[![rworkflows](https://github.com/GreenleafLab/ArchR/workflows/rworkflows/badge.svg)](https://github.com/GreenleafLab/ArchR/actions) +[![rworkflows](https://github.com/GreenleafLab/ArchR/workflows/rworkflows/badge.svg)](https://github.com/GreenleafLab/ArchR/actions) + [![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) ### ArchR has new features available for scATAC-seq Analysis From b2e5e0cea24bef169ab93e6d7d3d1acf5a13a997 Mon Sep 17 00:00:00 2001 From: bschilder Date: Fri, 1 Sep 2023 17:12:35 +0100 Subject: [PATCH 4/8] fix badges [skip ci] --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index f2cb1898..abe414c7 100755 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@

+ [![rworkflows](https://github.com/GreenleafLab/ArchR/workflows/rworkflows/badge.svg)](https://github.com/GreenleafLab/ArchR/actions) [![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) From ccf789d18d0601f4bec85832652db64522597fee Mon Sep 17 00:00:00 2001 From: "Brian M. Schilder" <34280215+bschilder@users.noreply.github.com> Date: Fri, 17 Nov 2023 11:25:25 +0000 Subject: [PATCH 5/8] Update rworkflows.yml --- .github/workflows/rworkflows.yml | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 34df233c..a989a0d2 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -14,8 +14,7 @@ name: rworkflows - RELEASE_** jobs: rworkflows: - permissions: - contents: write + permissions: write-all runs-on: ${{ matrix.config.os }} name: ${{ matrix.config.os }} (${{ matrix.config.r }}) container: ${{ matrix.config.cont }} @@ -26,8 +25,8 @@ jobs: - os: ubuntu-latest bioc: devel r: auto - cont: bioconductor/bioconductor_docker:devel - rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release + cont: ghcr.io/bioconductor/bioconductor_docker:devel + rspm: ~ - os: macOS-latest bioc: release r: auto @@ -45,13 +44,11 @@ jobs: run_rcmdcheck: ${{ true }} as_cran: ${{ true }} run_vignettes: ${{ true }} - has_testthat: ${{ true }} - run_covr: ${{ true }} + has_testthat: ${{ false }} + run_covr: ${{ false }} run_pkgdown: ${{ true }} has_runit: ${{ false }} has_latex: ${{ false }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - run_docker: ${{ false }} + run_docker: ${{ true }} DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} - runner_os: ${{ runner.os }} - cache_version: cache-v1 From 86cee8e5dfb02364a5f1c7f9f5f89387a4fa359d Mon Sep 17 00:00:00 2001 From: "Brian M. Schilder" <34280215+bschilder@users.noreply.github.com> Date: Fri, 17 Nov 2023 11:54:43 +0000 Subject: [PATCH 6/8] update rworkflows --- .Rbuildignore | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.Rbuildignore b/.Rbuildignore index 91114bf2..ea46df79 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,6 @@ ^.*\.Rproj$ ^\.Rproj\.user$ + +^node_modules$ +^package-lock\.json$ +^package\.json$ \ No newline at end of file From 3d2b4295f6373b21bb585f99e2bdfd60fdadf6f4 Mon Sep 17 00:00:00 2001 From: "Brian M. Schilder" <34280215+bschilder@users.noreply.github.com> Date: Fri, 17 Nov 2023 11:59:03 +0000 Subject: [PATCH 7/8] add newlines to .gitignore/.Rbuildignore --- .Rbuildignore | 2 +- .Rhistory | 3 +++ .gitignore | 2 +- 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index ea46df79..9ef387f4 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -3,4 +3,4 @@ ^node_modules$ ^package-lock\.json$ -^package\.json$ \ No newline at end of file +^package\.json$ diff --git a/.Rhistory b/.Rhistory index 8bd69bd8..6f0df125 100644 --- a/.Rhistory +++ b/.Rhistory @@ -333,3 +333,6 @@ setwd("~/Documents/GitHub/ArchR") pkgdown::build_site() warnings() pkgdown::build_site() +rworkflows::use_workflow() +rworkflows::use_workflow(force_new = T, run_docker = T) +covr::code_coverage() diff --git a/.gitignore b/.gitignore index 0a295973..09d1229a 100644 --- a/.gitignore +++ b/.gitignore @@ -2,4 +2,4 @@ .DS_Store .Rproj.user .Rhistory -.RData \ No newline at end of file +.RData From 894d14568610994c9bd1afa0d7fd214aaf8237fc Mon Sep 17 00:00:00 2001 From: "Brian M. Schilder" <34280215+bschilder@users.noreply.github.com> Date: Fri, 17 Nov 2023 12:01:14 +0000 Subject: [PATCH 8/8] remove .Rhistory from git tracking --- .Rbuildignore | 2 +- .Rhistory | 338 -------------------------------------------------- .gitignore | 10 +- 3 files changed, 9 insertions(+), 341 deletions(-) delete mode 100644 .Rhistory diff --git a/.Rbuildignore b/.Rbuildignore index 9ef387f4..2051f312 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,5 +1,5 @@ ^.*\.Rproj$ -^\.Rproj\.user$ +^\.Rproj\.user$. ^node_modules$ ^package-lock\.json$ diff --git a/.Rhistory b/.Rhistory deleted file mode 100644 index 6f0df125..00000000 --- a/.Rhistory +++ /dev/null @@ -1,338 +0,0 @@ ---- -title: "ArchR Hematopoiesis Tutorial" -author: "Jeffrey Granja" -date: "11/22/2019" -output: html_document ---- -```{r setup, include=FALSE} -knitr::opts_chunk$set(echo = TRUE) -``` -## R Markdown -knitr::opts_chunk$set(echo = TRUE) -knitr::opts_chunk$set(echo = TRUE) -summary(cars) -plot(pressure) -knitr::opts_chunk$set(echo = TRUE) -setwd("~/Documents/Heme_Tutorial/") -data("geneAnnoHg19") -data("genomeAnnoHg19") -threads <- 8 -pathFragments <- "Heme_Fragments" -inputFiles <- list.files(pathFragments, pattern = ".gz", full.names = TRUE) -names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathFragments, pattern = ".gz")) -inputFiles <- inputFiles[!grepl(".tbi", inputFiles)] -inputFiles -knitr::opts_chunk$set(echo = TRUE) -#Input Libraries -library(ArchR) -#Set/Create Working Directory to Folder -setwd("~/Documents/Heme_Tutorial/") -#Load Genome Annotations -data("geneAnnoHg19") -data("genomeAnnoHg19") -#Set Threads to be used -threads <- 8 -pathFragments <- "Heme_Fragments" -inputFiles <- list.files(pathFragments, pattern = ".gz", full.names = TRUE) -names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathFragments, pattern = ".gz")) -inputFiles <- inputFiles[!grepl(".tbi", inputFiles)] -inputFiles -#Input Libraries -library(ArchR) -#Set/Create Working Directory to Folder -setwd("~/Documents/Heme_Tutorial/") -#Load Genome Annotations -data("geneAnnoHg19") -data("genomeAnnoHg19") -#Set Threads to be used -threads <- 8 -knitr::opts_chunk$set(echo = TRUE) -opts_knit$set(root.dir = "~/Documents/Heme_Tutorial/") -library(knitr) -knitr::opts_chunk$set(echo = TRUE) -opts_knit$set(root.dir = "~/Documents/Heme_Tutorial/") -#Input Libraries -library(ArchR) -#Load Genome Annotations -data("geneAnnoHg19") -data("genomeAnnoHg19") -#Set Threads to be used -threads <- 8 -pathFragments <- "Heme_Fragments" -inputFiles <- list.files(pathFragments, pattern = ".gz", full.names = TRUE) -names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathFragments, pattern = ".gz")) -inputFiles <- inputFiles[!grepl(".tbi", inputFiles)] -inputFiles -#Input Libraries -library(ArchR) -#Load Genome Annotations -data("geneAnnoHg19") -data("genomeAnnoHg19") -#Set Threads to be used -threads <- 8 -library(knitr) -knitr::opts_chunk$set(echo = TRUE) -opts_knit$set(root.dir = "~/Documents/Heme_Tutorial/") -#Input Libraries -library(ArchR) -#Load Genome Annotations -data("geneAnnoHg19") -data("genomeAnnoHg19") -#Set Threads to be used -threads <- 8 -pathFragments <- "Heme_Fragments" -inputFiles <- list.files(pathFragments, pattern = ".gz", full.names = TRUE) -names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathFragments, pattern = ".gz")) -inputFiles <- inputFiles[!grepl(".tbi", inputFiles)] -inputFiles -#Input Libraries -library(ArchR) -#Load Genome Annotations -data("geneAnnoHg19") -data("genomeAnnoHg19") -#Set Threads to be used -threads <- 8 -library(knitr) -knitr::opts_chunk$set(echo = TRUE) -opts_knit$set(root.dir = "~/Documents/Heme_Tutorial/") -library(ArchR) -#Input Libraries -library(ArchR) -#Load Genome Annotations -data("geneAnnoHg19") -data("genomeAnnoHg19") -#Set Threads to be used -threads <- 8 -pathFragments <- "Heme_Fragments" -inputFiles <- list.files(pathFragments, pattern = ".gz", full.names = TRUE) -names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathFragments, pattern = ".gz")) -inputFiles <- inputFiles[!grepl(".tbi", inputFiles)] -inputFiles -library(knitr) -knitr::opts_chunk$set(echo = TRUE) -opts_knit$set(root.dir = "~/Documents/Heme_Tutorial/") -library(ArchR) -#Load Genome Annotations -data("geneAnnoHg19") -data("genomeAnnoHg19") -#Set Threads to be used -threads <- 8 -pathFragments <- "Heme_Fragments" -inputFiles <- list.files(pathFragments, pattern = ".gz", full.names = TRUE) -names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathFragments, pattern = ".gz")) -inputFiles <- inputFiles[!grepl(".tbi", inputFiles)] -inputFiles -ArrowFiles <- createArrowFiles( -inputFiles = inputFiles[3], -sampleNames = names(inputFiles), -geneAnno = geneAnnoHg19, -genomeAnno = genomeAnnoHg19, -threads = threads, -force = TRUE -) -ArrowFiles <- createArrowFiles( -inputFiles = inputFiles[3], -sampleNames = names(inputFiles)[3], -geneAnno = geneAnnoHg19, -genomeAnno = genomeAnnoHg19, -threads = threads, -force = TRUE -) -ls -```{r eval=TRUE, cache=TRUE} -ArrowFiles <- createArrowFiles( -inputFiles = inputFiles[3], -sampleNames = names(inputFiles)[3], -geneAnno = geneAnnoHg19, -genomeAnno = genomeAnnoHg19, -threads = threads, -addGeneScoreMat = FALSE, -addTileMat = FALSE, -force = TRUE -) -knitr::opts_chunk$set(echo = TRUE) -knitr::opts_chunk$set(eval = FALSE) -# Small fig.width -knitr::include_graphics("~/Documents/Heme_Tutorial/Heme_Tutorial/Plots/Plot-UMAP-TileLSI_Date-2019-11-22_Time-01-35-25.pdf") -# Small fig.width -knitr::include_graphics("~/Documents/Heme_Tutorial/Heme_Tutorial/Plots/Plot-UMAP-TileLSI_Date-2019-11-22_Time-01-35-25.pdf") -# Small fig.width -knitr::include_graphics("~/Documents/Heme_Tutorial/Heme_Tutorial/Plots/Plot-UMAP-TileLSI_Date-2019-11-22_Time-01-35-25.pdf") -getwd() -"/Users/jeffreygranja/Documents/Heme_Tutorial/Heme_Tutorial/Plots/Plot-UMAP-TileLSI_Date-2019-11-22_Time-01-35-25.pdf -# Small fig.width -knitr::include_graphics("/Users/jeffreygranja/Documents/Heme_Tutorial/Heme_Tutorial/Plots/Plot-UMAP-TileLSI_Date-2019-11-22_Time-01-35-25.pdf") -# Small fig.width -knitr::include_graphics("/Users/jeffreygranja/Documents/Heme_Tutorial/Heme_Tutorial/Plots/Plot-UMAP-TileLSI_Date-2019-11-22_Time-01-35-25.pdf") -"~/Documents/HemeAll/heme/Plots/Plot-Tracks_Date-2019-11-17_Time-17-52-02.pdf" -knitr::include_graphics(path.expand("~/Documents/HemeAll/heme/Plots/Plot-Tracks_Date-2019-11-17_Time-17-52-02.pdf")) -file.copy -list.files() -list.files() -system("cp ~/Documents/HemeAll/heme/Plots/Plot-Tracks_Date-2019-11-17_Time-17-52-02.pdf mychart.pdf") -knitr::include_graphics(path = "mychart.pdf") -"mychart.pdf" -knitr::include_graphics(path = "mychart.pdf")#path.expand("~/Documents/HemeAll/heme/Plots/Plot-Tracks_Date-2019-11-17_Time-17-52-02.pdf")) -knitr::include_graphics(path = "mychart.pdf") -knitr::opts_chunk$set(echo = TRUE) -```{r pressure, echo=FALSE, eval = FALSE} -sessionInfo() -head(sessionInfo()) -suppressPackageStartupMessages() -Sys.info() -.Platform -parallel::detectCores() -try(system("grep MemTotal /proc/meminfo", intern = TRUE), silent = TRUE) -ram = substring(system("sysctl hw.memsize", intern = TRUE), 13) #nocov -ram -ram / 10^9 -as.numeric(ram) / 10^9 -get_windows_ram = function() { -ram = try(system("grep MemTotal /proc/meminfo", intern = TRUE), silent = TRUE) -if (class(ram) != "try-error" && length(ram) != 0) { -ram = strsplit(ram, " ")[[1]] -ram = as.numeric(ram[length(ram) - 1]) -ram_size = ram -} else { -# Fallback: This was the old method I used -# It worked for Windows 7 and below. -ram_size = system("wmic MemoryChip get Capacity", intern = TRUE)[-1] -} -return(ram_size) -} -system_ram = function(os) { -if (length(grep("^linux", os))) { -cmd = "awk '/MemTotal/ {print $2}' /proc/meminfo" -ram = system(cmd, intern = TRUE) -} else if (length(grep("^darwin", os))) { -ram = substring(system("sysctl hw.memsize", intern = TRUE), 13) #nocov -} else if (length(grep("^solaris", os))) { -cmd = "prtconf | grep Memory" # nocov -ram = system(cmd, intern = TRUE) ## Memory size: XXX Megabytes # nocov -} else { -ram = get_windows_ram() # nocov -} -ram -} -#' Get the amount of RAM -#' -#' Attempt to extract the amount of RAM on the current machine. This is OS -#' specific: -#' \itemize{ -#' \item Linux: \code{proc/meminfo} -#' \item Apple: \code{system_profiler -detailLevel mini} -#' \item Windows: \code{memory.size()} -#' \item Solaris: \code{prtconf} -#' } -#' A value of \code{NA} is return if it isn't possible to determine the amount of RAM. -#' @export -#' @references The \code{print.bytes} function was taken from the \pkg{pryr} package. -#' @examples -#' ## Return (and pretty print) the amount of RAM -#' get_ram() -get_ram = function() { -os = R.version$os -ram = suppressWarnings(try(system_ram(os), silent = TRUE)) -if (class(ram) == "try-error" || length(ram) == 0) { -message("\t Unable to detect your RAM. # nocov -Please raise an issue at https://github.com/csgillespie/benchmarkme") # nocov -ram = structure(NA, class = "ram") # nocov -} else { -cleaned_ram = suppressWarnings(try(clean_ram(ram, os), silent = TRUE)) -if (class(cleaned_ram) == "try-error" || length(ram) == 0) { -message("\t Unable to detect your RAM. # nocov -Please raise an issue at https://github.com/csgillespie/benchmarkme") # nocov -ram = structure(NA, class = "ram") #nocov -} else { -ram = structure(cleaned_ram, class = "ram") -} -} -return(ram) -} -#' @rawNamespace S3method(print,ram) -print.ram = function(x, digits = 3, unit_system = c("metric", "iec"), ...) { -#unit_system = match.arg(unit_system) -unit_system = "metric" -base = switch(unit_system, metric = 1000, iec = 1024) -power = min(floor(log(abs(x), base)), 8) -if (is.na(x) || power < 1) { -unit = "B" -} else { -unit_labels = switch( -unit_system, -metric = c("kB", "MB", "GB", "TB", "PB", "EB", "ZB", "YB"), -iec = c("KiB", "MiB", "GiB", "TiB", "PiB", "EiB", "ZiB", "YiB") -) -unit = unit_labels[[power]] -x = x / (base^power) -} -formatted = format(signif(x, digits = digits), big.mark = ",", -scientific = FALSE, ...) -cat(unclass(formatted), " ", unit, "\n", sep = "") -invisible(paste(unclass(formatted), unit)) -} -get_ram() -plot(cars) -```{r eval = TRUE} -```{r} -suppressPackageStartupMessages(library(SnapATAC)) -suppressPackageStartupMessages(library(SnapATAC)) -suppressPackageStartupMessages(library(magrittr)) -setwd("/Volumes/JG_SSD_2/Data/Analysis/Tutorial/test-snap") -parallel::detectCores() -Sys.Date() -sessionInfo() -#5k -if(!file.exists("atac_pbmc_5k_nextgem_fragments.tsv.gz")){ -system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_5k_nextgem/atac_pbmc_5k_nextgem_fragments.tsv.gz") -system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_5k_nextgem/atac_pbmc_5k_nextgem_fragments.tsv.gz.tbi") -} -#10k -if(!file.exists("atac_pbmc_10k_nextgem_fragments.tsv.gz")){ -system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_10k_nextgem/atac_pbmc_10k_nextgem_fragments.tsv.gz") -system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_10k_nextgem/atac_pbmc_10k_nextgem_fragments.tsv.gz.tbi") -} -#Analysis of 10x Fragment Files -#Install pip install -user snaptools -snapTools <- "/Users/jeffreygranja/Library/Python/2.7/bin/snaptools" -#Fragment Files -fragFiles <- c( -"atac_pbmc_5k_nextgem_fragments.tsv.gz", -"atac_pbmc_10k_nextgem_fragments.tsv.gz" -) -#Input Genome -genome <- "hg19" -if(!file.exists(paste0(genome,".chrom.sizes"))){ -system(paste0("wget http://hgdownload.cse.ucsc.edu/goldenpath/",genome,"/bigZips/",genome,".chrom.sizes")) -} -#Download/Set Up 10x Fragment Files -#5k -if(!file.exists("atac_pbmc_5k_nextgem_fragments.tsv.gz")){ -system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_5k_nextgem/atac_pbmc_5k_nextgem_fragments.tsv.gz") -system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_5k_nextgem/atac_pbmc_5k_nextgem_fragments.tsv.gz.tbi") -} -#10k -if(!file.exists("atac_pbmc_10k_nextgem_fragments.tsv.gz")){ -system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_10k_nextgem/atac_pbmc_10k_nextgem_fragments.tsv.gz") -system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_10k_nextgem/atac_pbmc_10k_nextgem_fragments.tsv.gz.tbi") -} -#Analysis of 10x Fragment Files -#Install pip install -user snaptools -snapTools <- "/Users/jeffreygranja/Library/Python/2.7/bin/snaptools" -#Fragment Files -fragFiles <- c( -"atac_pbmc_5k_nextgem_fragments.tsv.gz", -"atac_pbmc_10k_nextgem_fragments.tsv.gz" -) -#Input Genome -genome <- "hg19" -if(!file.exists(paste0(genome,".chrom.sizes"))){ -system(paste0("wget http://hgdownload.cse.ucsc.edu/goldenpath/",genome,"/bigZips/",genome,".chrom.sizes")) -} -setwd("~/Documents/GitHub/ArchR") -pkgdown::build_site() -warnings() -pkgdown::build_site() -rworkflows::use_workflow() -rworkflows::use_workflow(force_new = T, run_docker = T) -covr::code_coverage() diff --git a/.gitignore b/.gitignore index 09d1229a..8c4bb375 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,11 @@ -.DS_Store -.DS_Store +# R project files +*.Rproj .Rproj.user +.Ruserdata +# History files .Rhistory +.Rapp.history +# Session Data files .RData +# User-specific files +.Ruserdata