Mercurial > repos > mingchen0919 > aurora_htseq_site

changeset 2:fad3864136c9 draft

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fix error
author mingchen0919
date Tue, 13 Mar 2018 09:49:58 -0400
parents 9be3a8754fb3
children 6e69c93fe491
files htseq_count_render.R htseq_count_site.yml htseq_count_site_render.R
diffstat 3 files changed, 86 insertions(+), 86 deletions(-) [+]
line wrap: on
line diff
--- a/htseq_count_render.R	Wed Mar 07 08:51:53 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-##============ 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(htmltools)
-#------------------------------------------------
-
-
-#------------get arguments into R--------------------
-# library(dplyr)
-# getopt_specification_matrix(extract_short_flags('')) %>%
-#   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_G",
-                            "X_f", "X_r", "X_S", "X_a", "X_T", "X_i", "X_m", "X_c", "X_O"),
-             short_flags = c("e", "o", "d", "s", "t", "A", "B", "G", "f", "r", "S",
-                             "a", "T", "i", "m", "c", "O"),
-             argument_mask_flags = c(1L, 1L, 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", "character", "character", "character",
-                                 "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_REPORT: path to galaxy output report
-# 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, '/htseq_count_site.Rmd ', OUTPUT_DIR, '/site_generator/htseq_count_site.Rmd'))
-system(paste0('cp -r ', TOOL_DIR, '/htseq_count_site.yml ', OUTPUT_DIR, '/site_generator/_site.yml'))
-system(paste0('cp -r ', TOOL_DIR, '/htseq_count_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=============================
\ No newline at end of file
--- a/htseq_count_site.yml	Wed Mar 07 08:51:53 2018 -0500
+++ b/htseq_count_site.yml	Tue Mar 13 09:49:58 2018 -0400
@@ -7,8 +7,8 @@
         - text: "Home"
           icon: fa-home
           href: index.html
-        - text: "TITLE 1"
-          href: htseq_count.html
+        - text: "htseq-count Analysis"
+          href: htseq_count_site.html
 output:
   html_document:
     theme: cosmo
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/htseq_count_site_render.R	Tue Mar 13 09:49:58 2018 -0400
@@ -0,0 +1,84 @@
+##============ 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(htmltools)
+#------------------------------------------------
+
+
+#------------get arguments into R--------------------
+# library(dplyr)
+# getopt_specification_matrix(extract_short_flags('')) %>%
+#   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_G",
+                            "X_f", "X_r", "X_S", "X_a", "X_T", "X_i", "X_m", "X_c", "X_O"),
+             short_flags = c("e", "o", "d", "s", "t", "A", "B", "G", "f", "r", "S",
+                             "a", "T", "i", "m", "c", "O"),
+             argument_mask_flags = c(1L, 1L, 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", "character", "character", "character",
+                                 "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_REPORT: path to galaxy output report
+# 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, '/htseq_count_site.Rmd ', OUTPUT_DIR, '/site_generator/htseq_count_site.Rmd'))
+system(paste0('cp -r ', TOOL_DIR, '/htseq_count_site.yml ', OUTPUT_DIR, '/site_generator/_site.yml'))
+system(paste0('cp -r ', TOOL_DIR, '/htseq_count_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=============================
\ No newline at end of file