Mercurial > repos > mingchen0919 > aurora_star

changeset 7:878d41e8fad9 draft

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planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311-dirty
author mingchen0919
date Thu, 26 Apr 2018 14:11:58 -0400
parents 9e058e122d05
children ba410e2de3a0
files expose-outputs.sh helper.R run-star.sh shell-script-template.sh star.Rmd star_render.R
diffstat 6 files changed, 171 insertions(+), 109 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/expose-outputs.sh	Thu Apr 26 14:11:58 2018 -0400
@@ -0,0 +1,6 @@
+# change directory to tool outputs directory
+cd ${REPORT_FILES_PATH}
+
+# copy outputs from tool outputs directory to corresponding galaxy output path
+cp star.html ${REPORT}
+cp Aligned.out.sorted.bam ${X_S}
\ No newline at end of file
--- a/helper.R	Wed Apr 18 11:13:37 2018 -0400
+++ b/helper.R	Thu Apr 26 14:11:58 2018 -0400
@@ -4,9 +4,14 @@
 #' The first column are short flags, the second column are argument masks, the third column
 #' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
 #' @param gtg_name the name of a running GTG.
-getopt_specification_matrix = function(specification_file, gtg_name = 'gtg', tool_dir = Sys.getenv('TOOL_DIR')) {
-  df = read.csv(paste0(tool_dir, '/', specification_file),
-                header = TRUE, stringsAsFactors = FALSE)
+getopt_specification_matrix = function(specification_file,
+                                       gtg_name = 'gtg',
+                                       tool_dir = Sys.getenv('TOOL_DIR')) {
+  df = read.csv(
+    paste0(tool_dir, '/', specification_file),
+    header = TRUE,
+    stringsAsFactors = FALSE
+  )
   # check if there are duplicated short flags
   short_flags = df[, 1]
   if (length(unique(short_flags)) < length(short_flags)) {
@@ -19,10 +24,12 @@
   long_flags = paste0('X_', df[, 1])
   
   # specification matrix
-  df2 = data.frame(long_flags = long_flags,
-                   short_flags = df[, 1],
-                   argument_mask = df[, 2],
-                   data_type = df[, 3])
+  df2 = data.frame(
+    long_flags = long_flags,
+    short_flags = df[, 1],
+    argument_mask = df[, 2],
+    data_type = df[, 3]
+  )
   
   as.matrix(df2)
 }
@@ -30,43 +37,46 @@
 
 
 #' \code{file_tree} generate file tree of a directory in the format of HTML lists.
-#' 
+#'
 #' @param dir the path to the directory for generating the file tree.
 #' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files.
 # define a recursive function to build html string of the file tree
-file_tree = function(dir = '.'){
+file_tree = function(dir = '.') {
   # get the OUTPUT_DIR folder data: dataset_NUMBER_files
   report_files_path = Sys.getenv('REPORT_FILES_PATH')
   output_dir = tail(strsplit(report_files_path, '/')[[1]], 1)
   
-  files = list.files(path = dir, recursive = FALSE, full.names = TRUE)
+  files = list.files(path = dir,
+                     recursive = FALSE,
+                     full.names = TRUE)
   # files also include directorys, need to remove directorys
   files = files[!dir.exists(files)]
-  dirs = list.dirs(path = dir, recursive = FALSE, full.names = TRUE)
-  # hide vakata-jstree-3.3.5 folder
-  #jstree_index = grep(pattern = 'vakata-jstree-3.3.5', x = dirs)
-  #dirs = dirs[-jstree_index]
-  tags$ul(
-    {
-      if (length(files) > 0) {
-        lapply(files, function(x){
-          path_end = tail(strsplit(x, '/')[[1]],1)
-          href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
-          li_item = tags$li(tags$a(path_end, href=href_path))
-          li_item$attribs = list('data-jstree'='{"icon":"jstree-file"}')
+  dirs = list.dirs(path = dir,
+                   recursive = FALSE,
+                   full.names = TRUE)
+  tags$ul({
+    if (length(files) > 0) {
+      lapply(files, function(x) {
+        path_end = tail(strsplit(x, '/')[[1]], 1)
+        href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
+        li_item = tags$li(tags$a(path_end, href = href_path))
+        li_item$attribs = list('data-jstree' = '{"icon":"jstree-file"}')
+        li_item
+      })
+    }
+  },
+  {
+    if (length(dirs) > 0) {
+      lapply(dirs, function(x) {
+        path_end = tail(strsplit(x, '/')[[1]], 1)
+        # hide vakata-jstree-3.3.5 folder
+        if (path_end != 'vakata-jstree-3.3.5') {
+          # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
+          li_item = tags$li(path_end, file_tree(x))
+          li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}')
           li_item
-        })
-      }
-    },
-    {
-      if (length(dirs) > 0) {
-        lapply(dirs, function(x){
-          x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
-          li_item = tags$li(x_path, file_tree(x))
-          li_item$attribs = list('data-jstree'='{"icon":"jstree-folder"}')
-          li_item
-        })
-      }
+        }
+      })
     }
-  )
+  })
 }
--- a/run-star.sh	Wed Apr 18 11:13:37 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-cd ${X_d}
-
-#--------- index genome --------
-# create genome directory for genome indexes
-mkdir -p ${X_d}/genomeDir
-
-cat >temp.sh <<EOF
-STAR \\
-  --runMode genomeGenerate \\
-  --genomeDir ${X_d}/genomeDir \\
-  --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \\
-  --sjdbGTFfile ${X_B} \\
-  --sjdbOverhang ${X_C} \\
-  > /dev/null 2>&1
-EOF
-
-grep -v None temp.sh > index-genome.sh
-
-# run star
-sh index-genome.sh
-
-#---- mapping ---------
-cat >temp.sh <<EOF
-STAR \\
-  --genomeDir ${X_d}/genomeDir \\
-  --readFilesIn \\
-  ${X_F} \\
-  ${X_R} \\
-  > /dev/null 2>&1
-EOF
-
-grep -v None temp.sh > mapping.sh
-
-# run mapping
-sh mapping.sh
-
-# remove temp.sh
-rm temp.sh
-
-#----- SAM to sorted BAM ------
-echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh
-sh sam2bam.sh
-
-#----- evaluate mapping -------
-echo "samtools flagstat Aligned.out.sorted.bam > flagstat.txt" > flagstat.sh
-sh flagstat.sh
-
-
-#====== expose outputs to galaxy history =======
-cp Aligned.out.sorted.bam ${X_S}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shell-script-template.sh	Thu Apr 26 14:11:58 2018 -0400
@@ -0,0 +1,47 @@
+# run SHELL_SCRIPT within tool outputs directory
+cd ${REPORT_FILES_PATH}
+
+#--------- index genome --------
+# create genome directory for genome indexes
+mkdir -p ${X_d}/genomeDir
+
+cat >temp.sh <<EOF
+STAR \\
+  --runMode genomeGenerate \\
+  --genomeDir ${X_d}/genomeDir \\
+  --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \\
+  --sjdbGTFfile ${X_B} \\
+  --sjdbOverhang ${X_C} \\
+  > /dev/null 2>&1
+EOF
+
+grep -v None temp.sh > index-genome.sh
+
+# run star
+sh index-genome.sh
+
+#---- mapping ---------
+cat >temp.sh <<EOF
+STAR \\
+  --genomeDir ${X_d}/genomeDir \\
+  --readFilesIn \\
+  ${X_F} \\
+  ${X_R} \\
+  > /dev/null 2>&1
+EOF
+
+grep -v None temp.sh > mapping.sh
+
+# run mapping
+sh mapping.sh
+
+# remove temp.sh
+rm temp.sh
+
+#----- SAM to sorted BAM ------
+echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh
+sh sam2bam.sh
+
+#----- evaluate mapping -------
+echo "samtools flagstat Aligned.out.sorted.bam > flagstat.txt" > flagstat.sh
+sh flagstat.sh
--- a/star.Rmd	Wed Apr 18 11:13:37 2018 -0400
+++ b/star.Rmd	Thu Apr 26 14:11:58 2018 -0400
@@ -5,6 +5,15 @@
       highlight: pygments
 ---
 
+```{css echo=FALSE}
+pre code, pre, code {
+  white-space: pre !important;
+  overflow-x: scroll !important;
+  word-break: keep-all !important;
+  word-wrap: initial !important;
+}
+```
+
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
 knitr::opts_knit$set(progress = FALSE)
 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
@@ -41,21 +50,57 @@
 </script>
 -----------------------------------------
 
-```{bash, echo=FALSE}
-sh ${TOOL_INSTALL_DIR}/run-star.sh
-```
 
 ## Job scripts
 
-* Index genome: [index-genome.sh](index-genome.sh)
-* Mapping: [mapping.sh](mapping.sh)
-* SAM to sorted BAM: [sam2bam.sh](sam2bam.sh)
-* Evaluate mapping: [flagstat.sh](flagstat.sh)
+```{bash, echo=FALSE}
+sh ${TOOL_INSTALL_DIR}/shell-script-template.sh
+```
+
+### Index genome
+
+```{r echo=FALSE,results='asis'}
+# display content of the job-script.sh file.
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/index-genome.sh')), sep = '\n')
+cat('\n```')
+```
+
+### Mapping
+
+```{r echo=FALSE,results='asis'}
+# display content of the job-script.sh file.
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/mapping.sh')), sep = '\n')
+cat('\n```')
+```
+
+### SAM to sorted BAM
 
-## Mapping evaluation
+```{r echo=FALSE,warning=FALSE,results='asis'}
+# display content of the job-script.sh file.
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/sam2bam.sh')), sep = '\n')
+cat('\n```')
+```
+
+### Mapping evaluation
 
-```{r, echo=FALSE}
-readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.txt'))
+```{r echo=FALSE,warning=FALSE,results='asis'}
+# display content of the job-script.sh file.
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.sh')), sep = '\n')
+cat('\n```')
+```
+
+
+### Mapping evaluation results
+
+```{r echo=FALSE,warning=FALSE,results='asis'}
+# display content of the job-script.sh file.
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.txt')), sep = '\n')
+cat('\n```')
 ```
 
 
--- a/star_render.R	Wed Apr 18 11:13:37 2018 -0400
+++ b/star_render.R	Thu Apr 26 14:11:58 2018 -0400
@@ -5,42 +5,46 @@
 sink(zz)
 sink(zz, type = 'message')
 
-#-------------------preparation -----------------
+#============== preparation ====================================
 options(stringsAsFactors = FALSE)
 # import libraries
-library(getopt)
-library(rmarkdown)
-library(htmltools)
+#------------------------------------------------------------------
+# ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES
+#------------------------------------------------------------------
+library('getopt')
+library('rmarkdown')
+library('htmltools')
+
+
 # load helper functions
 source(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/helper.R'))
 # import getopt specification matrix from a csv file
 opt = getopt(getopt_specification_matrix('getopt_specification.csv', 
                                          tool_dir=Sys.getenv('TOOL_INSTALL_DIR')))
-# define a unix variable versions for all input values. this is useful when we 
+# define environment variables for all input values. this is useful when we 
 # want to use input values by other programming language in r markdown
 do.call(Sys.setenv, opt[-1])
-#------------------------------------------------
+#===============================================================
 
 
-#-----------------render Rmd files --------------
+#======================== render Rmd files =========================
 # NOTICE: 
 #       we should copy all rmarkdown files from tool install directory to REPORT_FILES_PATH directory.
 #       and render rmarkdown files in the REPORT_FILES_PATH directory.
 file.copy(from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'),
           to = Sys.getenv('REPORT_FILES_PATH'), recursive = TRUE)
 system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}')
-# render Rmd files in order
+
+#----------------BELOW IS WHERE YOU NEED TO CUSTOMIZE ---------------------
 render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/star.Rmd'))
 # add more lines below if there are more Rmd files to be rendered
 
-#------------------------------------------
+#===============================================================
 
 
-#---------------- copy the output html to REPORT ----
-system(command = 'cp ${REPORT_FILES_PATH}/star.html ${REPORT}')
-# add more lines below if there are more output html files
-
-#==============the end==============
+#============== expose outputs to galaxy history ===============
+system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs.sh')
+#===============================================================
 
 
 ##--------end of code rendering .Rmd templates----------------