Mercurial > repos > mingchen0919 > aurora_demo_site

changeset 1:5808dc52afe8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
demo
author mingchen0919
date Mon, 12 Mar 2018 11:49:18 -0400
parents dd498df3f006
children
files aurora_demo_site.xml aurora_demo_site_1_python.Rmd aurora_demo_site_2_bash.Rmd aurora_demo_site_3_r.Rmd aurora_demo_site_bash.Rmd aurora_demo_site_python.Rmd aurora_demo_site_r.Rmd aurora_demo_site_render.R aurora_demo_site_site.yml
diffstat 9 files changed, 73 insertions(+), 87 deletions(-) [+]
line wrap: on
line diff
--- a/aurora_demo_site.xml	Mon Mar 12 10:02:53 2018 -0400
+++ b/aurora_demo_site.xml	Mon Mar 12 11:49:18 2018 -0400
@@ -12,12 +12,13 @@
         <regex match="XXX" source="stderr" level="warning"
                description="Check the warnings_and_errors.txt file for more details."/>
     </stdio>
-    <command><![CDATA[Rscript '${__tool_directory__}/aurora_demo_render.R'
+    <command><![CDATA[Rscript '${__tool_directory__}/aurora_demo_site_render.R'
 
       -r $row_number
       -c $column_number
 
       -R $report
+      -d $report.files_path
       -O $heatmap_data
 
       -T '${__tool_directory__}']]></command>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aurora_demo_site_1_python.Rmd	Mon Mar 12 11:49:18 2018 -0400
@@ -0,0 +1,24 @@
+---
+title: 'Python script'
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = TRUE, 
+  error = TRUE
+)
+```
+
+We first use Python code to generate a random data matrix and save the data into an output file.
+
+```{python}
+import numpy as np
+import os
+
+n_row = int(os.environ['X_r'])
+n_col = int(os.environ['X_c'])
+heatmap_data = np.power(10, np.random.randn(n_row, n_col))
+np.savetxt(os.environ['X_O'], heatmap_data)
+print(heatmap_data)
+```
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aurora_demo_site_2_bash.Rmd	Mon Mar 12 11:49:18 2018 -0400
@@ -0,0 +1,18 @@
+---
+title: 'Bash script'
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = TRUE, 
+  error = TRUE
+)
+```
+
+
+Then we use shell script to display the file content.
+
+```{bash}
+awk '{print $1, $2}' ${X_O}
+```
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aurora_demo_site_3_r.Rmd	Mon Mar 12 11:49:18 2018 -0400
@@ -0,0 +1,20 @@
+---
+title: 'R script'
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = TRUE, 
+  error = TRUE
+)
+```
+
+
+Finally, we use R script to import the data and generate a heatmap.
+
+```{r warning=FALSE, message=FALSE}
+heatmap_data = read.table(opt$X_O, header = FALSE, stringsAsFactors = FALSE)
+knitr::kable(heatmap_data)
+pheatmap::pheatmap(heatmap_data, cluster_rows = FALSE, cluster_cols = FALSE)
+```
--- a/aurora_demo_site_bash.Rmd	Mon Mar 12 10:02:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
----
-title: 'Bash script'
-output: html_document
----
-
-```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$set(
-  echo = TRUE, 
-  error = TRUE
-)
-```
-
-
-Then we use shell script to display the file content.
-
-```{bash}
-awk '{print $1, $2}' ${X_O}
-```
--- a/aurora_demo_site_python.Rmd	Mon Mar 12 10:02:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
----
-title: 'Python script'
-output: html_document
----
-
-```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$set(
-  echo = TRUE, 
-  error = TRUE
-)
-```
-
-We first use Python code to generate a random data matrix and save the data into an output file.
-
-```{python}
-import numpy as np
-import os
-
-n_row = int(os.environ['X_r'])
-n_col = int(os.environ['X_c'])
-heatmap_data = np.power(10, np.random.randn(n_row, n_col))
-np.savetxt(os.environ['X_O'], heatmap_data)
-print(heatmap_data)
-```
--- a/aurora_demo_site_r.Rmd	Mon Mar 12 10:02:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
----
-title: 'R script'
-output: html_document
----
-
-```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$set(
-  echo = TRUE, 
-  error = TRUE
-)
-```
-
-
-Finally, we use R script to import the data and generate a heatmap.
-
-```{r warning=FALSE, message=FALSE}
-heatmap_data = read.table(opt$X_O, header = FALSE, stringsAsFactors = FALSE)
-knitr::kable(heatmap_data)
-pheatmap::pheatmap(heatmap_data, cluster_rows = FALSE, cluster_cols = FALSE)
-```
--- a/aurora_demo_site_render.R	Mon Mar 12 10:02:53 2018 -0400
+++ b/aurora_demo_site_render.R	Mon Mar 12 11:49:18 2018 -0400
@@ -8,25 +8,10 @@
 #------------2. define environment variables-----
 spec_matrix = as.matrix(
   data.frame(stringsAsFactors=FALSE,
-             long_flags = c("X_r", "X_c", "X_R", "X_O", "X_T"),
-             short_flags = c("r", "c", "R", "O", "T"),
-             argument_mask_flags = c(1L, 1L, 1L, 1L, 1L),
-             data_type_flags = c("integer", "integer", "character", "character", "character")
-  )
-)
-opt = getopt(spec_matrix)
-do.call(Sys.setenv, opt[-1])
-#------------------------------------------------
-
-
-#------------1. collect input values in R--------
-#------------2. define environment variables-----
-spec_matrix = as.matrix(
-  data.frame(stringsAsFactors=FALSE,
-             long_flags = c("X_r", "X_c", "X_R", "X_O", "X_T"),
-             short_flags = c("r", "c", "R", "O", "T"),
-             argument_mask_flags = c(1L, 1L, 1L, 1L, 1L),
-             data_type_flags = c("integer", "integer", "character", "character", "character")
+             long_flags = c("X_r", "X_c", "X_R", "X_d", "X_O", "X_T"),
+             short_flags = c("r", "c", "R", "d", "O", "T"),
+             argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L),
+             data_type_flags = c("integer", "integer", "character", "character", "character", "character")
   )
 )
 opt = getopt(spec_matrix)
@@ -38,8 +23,8 @@
 # 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$X_o
+TOOL_DIR =   opt$X_T
+OUTPUT_REPORT = opt$X_R
 
 
 # create the output associated directory to store all outputs
--- a/aurora_demo_site_site.yml	Mon Mar 12 10:02:53 2018 -0400
+++ b/aurora_demo_site_site.yml	Mon Mar 12 11:49:18 2018 -0400
@@ -8,11 +8,11 @@
           icon: fa-home
           href: index.html
         - text: "Python"
-          href: aurora_demo_site_python.html
+          href: aurora_demo_site_1_python.html
         - text: "Bash"
-          href: aurora_demo_site_bash.html
+          href: aurora_demo_site_2_bash.html
         - text: "R"
-          href: aurora_demo_site_r.html
+          href: aurora_demo_site_3_r.html
 output:
   html_document:
     theme: cosmo