Mercurial > repos > mingchen0919 > aurora_deseq2_site
comparison DESeq_render.R @ 0:6f94b4b9de44 draft
planemo upload
author | mingchen0919 |
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date | Tue, 27 Feb 2018 23:57:53 -0500 |
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-1:000000000000 | 0:6f94b4b9de44 |
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1 ##============ Sink warnings and errors to a file ============== | |
2 ## use the sink() function to wrap all code within it. | |
3 ##============================================================== | |
4 zz = file('warnings_and_errors.txt') | |
5 sink(zz) | |
6 sink(zz, type = 'message') | |
7 | |
8 #------------import libraries-------------------- | |
9 options(stringsAsFactors = FALSE) | |
10 | |
11 library(getopt) | |
12 library(rmarkdown) | |
13 library(DESeq2) | |
14 library(pheatmap) | |
15 library(DT) | |
16 library(ggplot2) | |
17 library(genefilter) | |
18 library(RColorBrewer) | |
19 #------------------------------------------------ | |
20 | |
21 | |
22 #------------get arguments into R-------------------- | |
23 # getopt_specification_matrix(extract_short_flags('fastqc_report.xml')) %>% | |
24 # write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE) | |
25 | |
26 | |
27 spec_matrix = as.matrix( | |
28 data.frame(stringsAsFactors=FALSE, | |
29 long_flags = c("X_e", "X_o", "X_d", "X_s", "X_t", "X_P", "X_N", | |
30 "X_S", "X_p", "X_w"), | |
31 short_flags = c("e", "o", "d", "s", "t", "P", "N", "S", "p", "w"), | |
32 argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), | |
33 data_type_flags = c("character", "character", "character", "character", | |
34 "character", "character", "character", | |
35 "character", "character", "character") | |
36 ) | |
37 ) | |
38 opt = getopt(spec_matrix) | |
39 #---------------------------------------------------- | |
40 | |
41 | |
42 #-----------using passed arguments in R | |
43 # to define system environment variables--- | |
44 do.call(Sys.setenv, opt[-1]) | |
45 #---------------------------------------------------- | |
46 | |
47 #---------- often used variables ---------------- | |
48 # OUTPUT_REPORT: path to galaxy output report | |
49 # OUTPUT_DIR: path to the output associated directory, which stores all outputs | |
50 # TOOL_DIR: path to the tool installation directory | |
51 OUTPUT_DIR = opt$X_d | |
52 TOOL_DIR = opt$X_t | |
53 OUTPUT_REPORT = opt$X_o | |
54 | |
55 | |
56 # create the output associated directory to store all outputs | |
57 dir.create(OUTPUT_DIR, recursive = TRUE) | |
58 | |
59 #-----------------render site-------------- | |
60 # copy site generating materials into OUTPUT_DIR | |
61 dir.create(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE) | |
62 command_cp = paste0('cp -r ', TOOL_DIR, '/DESeq_0*.Rmd ', OUTPUT_DIR, '/site_generator') | |
63 system(command_cp) | |
64 system(paste0('cp -r ', TOOL_DIR, '/DESeq_site.yml ', OUTPUT_DIR, '/site_generator/_site.yml')) | |
65 system(paste0('cp -r ', TOOL_DIR, '/DESeq_index.Rmd ', OUTPUT_DIR, '/site_generator/index.Rmd')) | |
66 # render site to OUTPUT_DIR/_site, this is configured in the "_site.yml" file | |
67 dir.create(paste0(OUTPUT_DIR, '/_site')) | |
68 render_site(input = paste0(OUTPUT_DIR, '/site_generator')) | |
69 # remove site generating materials from output associated directory | |
70 print(unlink(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE)) | |
71 # move _site/* into output associated directory | |
72 move_cmd = paste0('mv ', OUTPUT_DIR, '/_site/* ', OUTPUT_DIR) | |
73 system(move_cmd) | |
74 #------------------------------------------ | |
75 | |
76 #-----link index.html to output----- | |
77 cp_index = paste0('cp ', OUTPUT_DIR, '/index.html ', OUTPUT_REPORT) | |
78 system(cp_index) | |
79 #----------------------------------- | |
80 | |
81 #==============the end============== | |
82 | |
83 | |
84 ##--------end of code rendering .Rmd templates---------------- | |
85 sink() | |
86 ##=========== End of sinking output============================= |