## ----include=FALSE------------------------------------------------------- knitr::opts_chunk$set(eval = FALSE) library("sevenbridges") ## ------------------------------------------------------------------------ # if (!require("devtools", quietly = TRUE)) install.packages("devtools") # source("https://bioconductor.org/biocLite.R") # devtools::install_github( # "sbg/sevenbridges-r", build_vignettes = TRUE, # repos = BiocInstaller::biocinstallRepos(), dependencies = TRUE) ## ------------------------------------------------------------------------ # browseVignettes(package = "sevenbridges") ## ------------------------------------------------------------------------ # a <- Auth(token = "your_token", platform = "cgc") ## ------------------------------------------------------------------------ # a <- Auth(from = "file", profile_name = "cgc") # # # remove old project # # a$project(id = "tengfei/hackathon")$delete() ## ------------------------------------------------------------------------ # sbg_set_env("https://cgc-api.sbgenomics.com/v2", "your_token") ## ------------------------------------------------------------------------ # a <- Auth(from = "env") ## ------------------------------------------------------------------------ # (b <- a$billing()) # # a single billing group is showing ## ------------------------------------------------------------------------ # (p <- a$project_new("hackathon", # billing_group_id = b$id, # description = "This project is for CGC hackathon")) ## ------------------------------------------------------------------------ # # p$delete() ## ---- comment = "", eval = TRUE------------------------------------------ rbx <- Tool(id = "runif", label = "runif", hints = requirements(docker(pull = "rocker/r-base"), cpu(1), mem(2000)), baseCommand = "Rscript -e 'runif(100)'", stdout = "output.txt", outputs = output(id = "random", glob = "*.txt")) rbx$toJSON(pretty = TRUE) ## ---- eval = TRUE-------------------------------------------------------- # provide scripts # make a new script file fd <- fileDef(name = "runif.R", content = "sed.seed(1) runif(100)") rbx <- Tool(id = "runif", label = "runif", hints = requirements(docker(pull = "rocker/r-base"), cpu(1), mem(2000)), requirements = requirements(fd), baseCommand = "Rscript runif.R", # run script you created. stdout = "output.txt", outputs = output(id = "random", glob = "*.txt")) ## ---- eval = TRUE-------------------------------------------------------- fl <- system.file("docker/rnaseqGene", "Dockerfile", package = "sevenbridges") ## ----comment='', eval = TRUE--------------------------------------------- cat(readLines(fl), sep = '\n') ## ---- eval = TRUE-------------------------------------------------------- fl <- system.file("docker/rnaseqGene/src", "performDE.R", package = "sevenbridges") ## ----comment='', eval = TRUE--------------------------------------------- cat(readLines(fl), sep = '\n') ## ---- eval = TRUE-------------------------------------------------------- fl <- system.file("docker/rnaseqGene/report", "rnaseqGene.Rmd", package = "sevenbridges") ## ----comment = "", eval = TRUE------------------------------------------- cat(readLines(fl, n = 50), sep = '\n') ## ---- eval = TRUE-------------------------------------------------------- rbx <- Tool(id = "rnaseqGene", label = "rnaseqgene", description = "A RNA-seq Differiencial Expression Flow and Report", hints = requirements(docker(pull = "tengfei/rnaseqgene"), cpu(1), mem(2000)), baseCommand = "performDE.R", inputs = list( input( id = "bamfiles", label = "bam files", description = "a list of bam files", type = "File...", ## or type = ItemArray("File") prefix = "--bamfiles", itemSeparator = "," ), input( id = "design", label = "design matrix", type = "File", prefix = "--design" ), input( id = "gtffile", label = "gene feature files", type = "File", prefix = "--gtffile" ), input( id = "format", label = "report foramt html or pdf", type = enum("format", c("pdf", "html")), prefix = "--format" ) ), outputs = list( output(id = "report", label = "report", description = "A reproducible report created by Rmarkdown", glob = Expression(engine = "#cwl-js-engine", script = "x = $job[['inputs']][['format']]; if(x == 'undefined' || x == null){ x = 'html'; }; 'rnaseqGene.' + x")), output(id = "heatmap", label = "heatmap", description = "A heatmap plot to show the Euclidean distance between samples", glob = "heatmap.pdf"), output(id = "count", label = "count", description = "Reads counts matrix", glob = "count.csv"), output(id = "de", label = "Differential expression table", description = "Differential expression table", glob = "de.csv") )) ## ----comment = "", eval = TRUE------------------------------------------- rbx rbx$toJSON(pretty = TRUE) rbx$toJSON() # or write to external file # fl <- "~/Downloads/rnaseqGene.json" # write(rbx$toJSON(pretty = TRUE), fl) ## ------------------------------------------------------------------------ # # add App you just created # (rna.app <- p$app_add("rnaseqgene", rbx)) ## ------------------------------------------------------------------------ # fl <- system.file("extdata", "sample1.fastq", package = "sevenbridges") # (p <- a$project(id = "tengfei/quickstart")) # # by default load .meta for the file # p$upload(fl, overwrite = TRUE) # # pass metadata # p$upload(fl, overwrite = TRUE, metadata = list(library_id = "testid2", platform = "Illumina x11")) # # rename # p$upload(fl, overwrite = TRUE, name = "sample_new_name.fastq", # metadata = list(library_id = "new_id")) # # # upload folder # dir.ext <- system.file("extdata", package = "sevenbridges") # p$upload(dir.ext, overwrite = TRUE) # # # upload file list # fls <- list.files(dir.ext, recursive = TRUE, full.names = TRUE) # p$upload(fls, overwrite = TRUE) ## ---- comment = "", eval = TRUE------------------------------------------ download.fl <- system.file("extdata/download.txt", package = "sevenbridges") cat(readLines(download.fl), sep = '\n') ## ------------------------------------------------------------------------ # td <- tempfile() # dir.create(td) # for(f in readLines(download.fl)){ # download.file(f, file.path(td, basename(f))) # } # # double check # list.files(td) # # upload to the project you created # p$upload(td) ## ------------------------------------------------------------------------ # # get file id you need as inout # (bamfiles.in <- p$file(".bam")) # (design.in <- p$file("sample_table.csv")) # (gtf.in <- p$file("Homo_sapiens.GRCh37.75_subset.gtf")) ## ------------------------------------------------------------------------ # bam1 <- p$file("SRR1039516_subset.bam") # bam2 <- p$file("SRR1039512_subset.bam") # bamfiles.in2 <- list(bam1, bam2) ## ------------------------------------------------------------------------ # # add a new Task # (tsk <- p$task_add(name = "RNA DE report new", # description = "RNA DE analysis report", # app = rna.app$id, # inputs = list(bamfiles = bamfiles.in, # design = design.in, # gtffile = gtf.in))) # # # don't forget to run a draft task # tsk$run() ## ------------------------------------------------------------------------ # # # monitor the task # # tsk$monitor() ## ------------------------------------------------------------------------ # setTaskHook("completed", function() { # tsk$download("~/Downloads") # }) # tsk$monitor() ## ------------------------------------------------------------------------ # tsk$download("~/Downloads") ## ------------------------------------------------------------------------ # # batch by items # (tsk <- p$task_add(name = "RNA DE report new batch 2", # description = "RNA DE analysis report", # app = rna.app$id, # batch = batch(input = "bamfiles"), # inputs = list(bamfiles = bamfiles.in, # design = design.in, # gtffile = gtf.in))) # # # batch by metadata, input files has to have metadata fields specified # (tsk <- p$task_add(name = "RNA DE report new batch 3", # description = "RNA DE analysis report", # app = rna.app$id, # batch = batch(input = "fastq", # c("metadata.sample_id", "metadata.library_id")), # inputs = list(bamfiles = bamfiles.in, # design = design.in, # gtffile = gtf.in))) ## ----comment = "", eval = TRUE------------------------------------------- fl <- system.file("docker/reporttool/rabix/reporttool.json", package = "sevenbridges") cat(readLines(fl), sep= "\n") ## ------------------------------------------------------------------------ # # directly add json file # p <- a$project(id = "tengfei/hackathon") # (report.app <- p$app_add("report-tool", fl)) ## ----comment = "", eval = TRUE------------------------------------------- fl <- system.file("docker/reporttool/Dockerfile", package = "sevenbridges") cat(readLines(fl), sep= "\n") ## ----comment = "", eval = FALSE------------------------------------------ # fl <- system.file("docker/reporttool/src/report.R", # package = "sevenbriges") # cat(readLines(fl), sep= "\n") ## ----comment = "", eval = FALSE------------------------------------------ # fl <- system.file("docker/reporttool/rabix/generator.R", # package = "sevenbriges") # cat(readLines(fl), sep= "\n") ## ------------------------------------------------------------------------ # browseVignettes("sevenbridges")