Mercurial > repos > mingchen0919 > aurora_deseq2_site
view deseq2_site_render.R @ 2:706ecfe0bac3 draft
initial 2.2.0
author | mingchen0919 |
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date | Fri, 09 Mar 2018 08:53:17 -0500 |
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##============ Sink warnings and errors to a file ============== ## use the sink() function to wrap all code within it. ##============================================================== zz = file('warnings_and_errors.txt') sink(zz) sink(zz, type = 'message') #------------import libraries-------------------- options(stringsAsFactors = FALSE) library(getopt) library(rmarkdown) library(ggplot2) library(plotly) library(htmltools) library(DESeq2) library(pheatmap) library(DT) #------------------------------------------------ #------------get arguments into R-------------------- # library(dplyr) # getopt_specification_matrix(extract_short_flags('deseq2.xml')) %>% # write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE) spec_matrix = as.matrix( data.frame(stringsAsFactors=FALSE, long_flags = c("X_e", "X_o", "X_d", "X_s", "X_t", "X_A", "X_B", "X_C", "X_D", "X_E", "X_F", "X_G", "X_H", "X_I", "X_J"), short_flags = c("e", "o", "d", "s", "t", "A", "B", "C", "D", "E", "F", "G", "H", "I", "J"), argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), data_type_flags = c("character", "character", "character", "character", "character", "character", "character", "character", "character", "character", "character", "character", "character", "double", "character") ) ) opt = getopt(spec_matrix) #---------------------------------------------------- #-----------using passed arguments in R # to define system environment variables--- do.call(Sys.setenv, opt[-1]) #---------------------------------------------------- #---------- often used variables ---------------- # OUTPUT_DIR: path to the output associated directory, which stores all outputs # TOOL_DIR: path to the tool installation directory OUTPUT_DIR = opt$X_d TOOL_DIR = opt$X_t OUTPUT_REPORT = opt$X_o # create the output associated directory to store all outputs dir.create(OUTPUT_DIR, recursive = TRUE) #-----------------render site-------------- # copy site generating materials into OUTPUT_DIR dir.create(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE) system(paste0('cp -r ', TOOL_DIR, '/deseq2_0*.Rmd ', OUTPUT_DIR, '/site_generator/')) system(paste0('cp -r ', TOOL_DIR, '/deseq2_site_site.yml ', OUTPUT_DIR, '/site_generator/_site.yml')) system(paste0('cp -r ', TOOL_DIR, '/deseq2_site_index.Rmd ', OUTPUT_DIR, '/site_generator/index.Rmd')) # render site to OUTPUT_DIR/_site, this is configured in the "_site.yml" file render_site(input = paste0(OUTPUT_DIR, '/site_generator')) # remove site generating materials from output associated directory unlink(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE) # move _site/* into output associated directory move_cmd = paste0('mv ', OUTPUT_DIR, '/_site/* ', OUTPUT_DIR) system(move_cmd) #------------------------------------------ #-----link index.html to output----- cp_index = paste0('cp ', OUTPUT_DIR, '/index.html ', OUTPUT_REPORT) system(cp_index) #----------------------------------- #==============the end============== ##--------end of code rendering .Rmd templates---------------- sink() ##=========== End of sinking output=============================