Mercurial > repos > mingchen0919 > aurora_htseq

comparison rmarkdown_report.Rmd @ 2:e08dd15646c6 draft

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planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
author mingchen0919
date Thu, 13 Dec 2018 23:45:31 -0500
parents 803f4888f36a
children
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1:fd547674f29f 2:e08dd15646c6
7 7
8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} 8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
9 knitr::opts_chunk$set(error = TRUE, echo = FALSE) 9 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
10 ``` 10 ```
11 11
12 ```{css echo=FALSE} 12 ```{css, echo=FALSE}
13 # code chunks scrollable
14 pre code, pre, code { 13 pre code, pre, code {
15 white-space: pre !important; 14 white-space: pre !important;
16 overflow-x: scroll !important; 15 overflow-x: scroll !important;
17 word-break: keep-all !important; 16 word-break: keep-all !important;
18 word-wrap: initial !important; 17 word-wrap: initial !important;
19 } 18 }
20 ``` 19 ```
21
22 20
23 ```{r, echo=FALSE} 21 ```{r, echo=FALSE}
24 # to make the css theme to work, <link></link> tags cannot be added directly 22 # to make the css theme to work, <link></link> tags cannot be added directly
25 # as <script></script> tags as below. 23 # as <script></script> tags as below.
26 # it has to be added using a code chunk with the htmltool functions!!! 24 # it has to be added using a code chunk with the htmltool functions!!!
31 29
32 ```{r, eval=FALSE, echo=FALSE} 30 ```{r, eval=FALSE, echo=FALSE}
33 # this code chunk is purely for adding comments 31 # this code chunk is purely for adding comments
34 # below is to add jQuery and jstree javascripts 32 # below is to add jQuery and jstree javascripts
35 ``` 33 ```
36 <script src="https://code.jquery.com/jquery-3.3.1.min.js"></script> 34
37 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script> 35 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
38 36
37
39 ```{r, eval=FALSE, echo=FALSE} 38 ```{r, eval=FALSE, echo=FALSE}
40 # The script below is used to avoid conflicts between different javascript labraries 39 # this code chunk is purely for adding comments
41 ```
42
43 <script>
44 jQuery.noConflict();
45
46 jQuery( document ).ready(function( $ ) {
47 // You can use the locally-scoped $ in here as an alias to jQuery.
48 $( "jstree" ).hide();
49 });
50
51 // The $ variable in the global scope has the prototype.js meaning.
52 window.onload = function(){
53 var mainDiv = $( "main" );
54 }
55 </script>
56
57 ---
58 # javascript code below is to build the file tree interface 40 # javascript code below is to build the file tree interface
59 # see this for how to implement opening hyperlink: https://stackoverflow.com/questions/18611317/how-to-get-i-get-leaf-nodes-in-jstree-to-open-their-hyperlink-when-clicked-when 41 # see this for how to implement opening hyperlink: https://stackoverflow.com/questions/18611317/how-to-get-i-get-leaf-nodes-in-jstree-to-open-their-hyperlink-when-clicked-when
60 --- 42 ```
61 <script> 43 <script>
62 $(function () { 44 jQuery(function () {
63 // create an instance when the DOM is ready 45 // create an instance when the DOM is ready
64 $('#jstree').jstree().bind("select_node.jstree", function (e, data) { 46 jQuery('#jstree').jstree().bind("select_node.jstree", function (e, data) {
65 window.open( data.node.a_attr.href, data.node.a_attr.target ) 47 window.open( data.node.a_attr.href, data.node.a_attr.target )
66 }); 48 });
67 }); 49 });
68 </script> 50 </script>
69 51
52
53 ```{r, eval=FALSE, echo=FALSE}
70 --- 54 ---
71 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE 55 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
72 --- 56 ---
57 ```
73 58
74 ## Job script 59 ## Job script
75 60
76 ```{bash, echo=FALSE} 61 ```{bash, echo=FALSE}
77 sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh > ${REPORT_FILES_PATH}/log.txt 2>&1 62 sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh > ${REPORT_FILES_PATH}/log.txt 2>&1