# HG changeset patch
# User mingchen0919
# Date 1520953521 14400
# Node ID acb9908e68e4fb69a9d83e6575cf2104c128a42d
# Parent  b9c9d1dacda66f28b3ddbe4858eb6faa5a4ebbf5
2.1.1

diff -r b9c9d1dacda6 -r acb9908e68e4 _site.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/_site.yml	Tue Mar 13 11:05:21 2018 -0400
@@ -0,0 +1,37 @@
+name: "FastQC Website"
+output_dir: "../_site"
+navbar:
+    title: "FastQC"
+    type: inverse
+    left:
+        - text: "Home"
+          icon: fa-home
+          href: index.html
+        - text: "Evaluation Overview"
+          href: 01_evaluation_overview.html
+        - text: "Evaluation by data module"
+          menu:
+            - text: "Per Base Sequence Quality"
+              href: 02_per_base_sequence_quality.html
+            - text: "Per Tile Sequence Quality"
+              href: 03_per_tile_sequence_quality.html
+            - text: "Per Sequence Quality Score"
+              href: 04_per_sequence_quality_score.html
+            - text: "Per Base Sequence Content"
+              href: 05_per_base_sequence_content.html
+            - text: "Per Sequence GC Content"
+              href: 06_per_sequence_gc_content.html
+            - text: "Per Base N Content"
+              href: 07_per_base_n_content.html
+            - text: "Sequence Length Distribution"
+              href: 08_sequence_length_distribution.html
+            - text: "Sequence Duplication Levels"
+              href: 09_sequence_duplication_levels.html
+            - text: "Adapter Content"
+              href: 10_adapter_content.html
+            - text: "Kmer Content"
+              href: 11_kmer_content.html
+output:
+  html_document:
+    theme: cosmo
+    highlight: textmate
\ No newline at end of file
diff -r b9c9d1dacda6 -r acb9908e68e4 fastqc_site.xml
--- a/fastqc_site.xml	Fri Mar 09 17:47:50 2018 -0500
+++ b/fastqc_site.xml	Tue Mar 13 11:05:21 2018 -0400
@@ -1,4 +1,4 @@
-<tool name="Aurora Fastqc site" id='aurora_fastqc_site' version="2.1.0">
+<tool name="Aurora Fastqc site" id='aurora_fastqc_site' version="2.1.1">
     <description>
         Evaluate short reads with FastQC software on a single or a paired of untrimmed and trimmed reads
         files.
@@ -6,7 +6,7 @@
     <requirements>
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
-        <requirement type="package" version="1.3">r-rmarkdown</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
         <requirement type="package" version="1.8.4">r-plyr</requirement>
         <requirement type="package" version="1.1.0">r-stringr</requirement>
         <requirement type="package" version="0.2">r-dt</requirement>
@@ -14,8 +14,6 @@
         <requirement type="package" version="4.5.6">r-plotly</requirement>
         <requirement type="package" version="0.3.5">r-htmltools</requirement>
         <requirement type="package" version="0.11.5">fastqc</requirement>
-        <requirement type="package" version="0.9.10">xorg-libxrender</requirement>
-        <requirement type="package" version="1.2.2">xorg-libsm</requirement>
         <requirement type="package" version="6.0">unzip</requirement>
     </requirements>
     <stdio>
diff -r b9c9d1dacda6 -r acb9908e68e4 fastqc_site_render.R
--- a/fastqc_site_render.R	Fri Mar 09 17:47:50 2018 -0500
+++ b/fastqc_site_render.R	Tue Mar 13 11:05:21 2018 -0400
@@ -34,22 +34,37 @@
   )
 )
 opt = getopt(spec_matrix)
+#----------------------------------------------------
 
-# using passed arguments in R to define system environment variables
+
+#-----------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(opt$X_d, recursive = TRUE)
+dir.create(OUTPUT_DIR, recursive = TRUE)
 
-#-----------------render site--------------
-# copy site generating materials into folder "_site" within the output associated directory
-file.copy(opt$X_t, opt$X_d, recursive = TRUE)
-# render site to the output associated directory
-render_site(input = paste0(opt$X_d, '/aurora_fastqc_site'))
+# copy site generating materials into OUTPUT_DIR
+dir.create(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE)
+system(paste0('cp -r ', TOOL_DIR, '/*.Rmd ', OUTPUT_DIR, '/site_generator/'))
+system(paste0('cp -r ', TOOL_DIR, '/_site.yml ', OUTPUT_DIR, '/site_generator/_site.yml'))
+system(paste0('cp -r ', TOOL_DIR, '/index.Rmd ', OUTPUT_DIR, '/site_generator/index.Rmd'))
+# render site to OUTPUT_DIR/_site, this is configured in the "_site.yml" file
+render_site(input = paste0(OUTPUT_DIR, '/site_generator'))
 # remove site generating materials from output associated directory
-unlink(paste0(opt$X_d, '/aurora_fastqc_site'), recursive = TRUE)
+unlink(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE)
 # move _site/* into output associated directory
-move_cmd = paste0('mv ', opt$X_d, '/_site/* ', opt$X_d)
+move_cmd = paste0('mv ', OUTPUT_DIR, '/_site/* ', OUTPUT_DIR)
 system(move_cmd)
 #------------------------------------------