Mercurial > repos > mingchen0919 > aurora_bdss_url
changeset 0:b12c945daf86 draft
planemo upload for repository https://github.com/feltus/BDSS
author | mingchen0919 |
---|---|
date | Mon, 11 Jun 2018 23:04:53 -0400 |
parents | |
children | a110308993be |
files | build-and-run-job-scripts.sh command-line-arguments.csv expose-outputs-to-galaxy-history.sh rmarkdown_report.Rmd rmarkdown_report.xml rmarkdown_report_render.R vakata-jstree-3.3.5.zip |
diffstat | 7 files changed, 332 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build-and-run-job-scripts.sh Mon Jun 11 23:04:53 2018 -0400 @@ -0,0 +1,19 @@ +# run job scripts within the tool outputs directory +cd ${REPORT_FILES_PATH} + +#========== build and run job 1 script ============ +cat >bdss-download.sh <<EOF +#------------ BELOW IS WHERE YOU WRITE YOUR OWN SHELL SCRIPT -------------- +export PATH=/main/sites/galaxy/galaxy/tools/_conda/bin:$PATH + +for $u in $(echo $X_u | sed "s/,/ /g"); +do + echo "bdss transfer --destination download_dir -u $u" +done + + +#------------ END OF SHELL SCRIPT ------------------------------------------ +EOF + + +sh bdss-download.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/command-line-arguments.csv Mon Jun 11 23:04:53 2018 -0400 @@ -0,0 +1,4 @@ +short flag,argument mask,data type,variable name +o,1,character,report +d,1,character,report.files_path +u,1,character,urls \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/expose-outputs-to-galaxy-history.sh Mon Jun 11 23:04:53 2018 -0400 @@ -0,0 +1,11 @@ +# change directory to tool outputs directory +cd ${REPORT_FILES_PATH} + +# copy outputs from tool outputs directory to corresponding galaxy output path +if [ -e "rmarkdown_report.html" ]; then + cp rmarkdown_report.html ${REPORT} +fi + +if [ -e "index.html" ]; then + cp index.html ${REPORT} +fi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmarkdown_report.Rmd Mon Jun 11 23:04:53 2018 -0400 @@ -0,0 +1,68 @@ +--- +title: 'Aurora Tool Report' +output: + html_document: + highlight: pygments +--- + +```{r setup, include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_chunk$set(error = TRUE, echo = FALSE) +``` + +```{css echo=FALSE} +# code chunks scrollable +pre code, pre, code { + white-space: pre !important; + overflow-x: scroll !important; + word-break: keep-all !important; + word-wrap: initial !important; +} +``` + + +```{r, echo=FALSE} +# to make the css theme to work, <link></link> tags cannot be added directly +# as <script></script> tags as below. +# it has to be added using a code chunk with the htmltool functions!!! +css_link = tags$link() +css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css") +css_link +``` + +```{r, eval=FALSE, echo=FALSE} +# this code chunk is purely for adding comments +# below is to add jQuery and jstree javascripts +``` +<script src="https://code.jquery.com/jquery-3.3.1.min.js"></script> +<script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script> + +--- +# javascript code below is to build the file tree interface +# 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 +--- +<script> + $(function () { + // create an instance when the DOM is ready + $('#jstree').jstree().bind("select_node.jstree", function (e, data) { + window.open( data.node.a_attr.href, data.node.a_attr.target ) + }); + }); +</script> + +--- +# ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE +--- + +## BDSS download + +## Job script + +```{bash, echo=FALSE} +sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh > ${REPORT_FILES_PATH}/log.txt 2>&1 +``` + +```{r echo=FALSE, comment='', results='asis'} +cat('```bash\n') +cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/bdss-download.sh')), sep = '\n') +cat('\n```') +```
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmarkdown_report.xml Mon Jun 11 23:04:53 2018 -0400 @@ -0,0 +1,73 @@ +<tool name="aurora_bdss_url" id='aurora_bdss_url_report' version="1.0.0"> + <description> + some description + </description> + <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="1.6">r-rmarkdown</requirement> + </requirements> + <command><![CDATA[ + + ######### each aurora tool generates a html file and have an files path directory associated with it. + mkdir -p $report.files_path && + + ######### three important paths: + ######### 1. path to tool installation directory + ######### 2. path to report html + ######### 3. path to files_path directory associated with the report output. + export TOOL_INSTALL_DIR='${__tool_directory__}' && + export REPORT='$report' && + export REPORT_FILES_PATH='$report.files_path' && + + ############ create a hidden file to store r markdown rendering log + touch $report.files_path/.r_rendering.log.txt && + + ############ finally run the render.R script + Rscript '${__tool_directory__}/rmarkdown_report_render.R' + + -o $report + -d $report.files_path + + -u $urls + + + ]]></command> + <inputs> + <param type="text" name="urls" area="true" size="5x25" label="URLs to data files" /> + </inputs> + <outputs> + <data format="html" name="report" label="${tool.name} report on ${on_string}"/> + <data name="output" label="BDSS downloaded data"> + <discover_datasets pattern="__name_and_ext__" directory="download_dir" visible="true"/> + </data> + </outputs> + <citations> + <citation type="bibtex"><![CDATA[ + @article{allaire2016rmarkdown, + title={rmarkdown: Dynamic Documents for R, 2016}, + author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff + and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, + journal={R package version 0.9}, + volume={6}, + year={2016} + } + ]]></citation> + <citation type="bibtex"><![CDATA[ + @book{xie2015dynamic, + title={Dynamic Documents with R and knitr}, + author={Xie, Yihui}, + volume={29}, + year={2015}, + publisher={CRC Press} + } + ]]></citation> + <citation type="bibtex"><![CDATA[ + @online{jstree, + author={Bozhanov, Ivan}, + year = 2018, + url = {https://www.jstree.com/} + } + ]]></citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rmarkdown_report_render.R Mon Jun 11 23:04:53 2018 -0400 @@ -0,0 +1,157 @@ +##============ Sink warnings and errors to a file ============== +## use the sink() function to wrap all code within it. +##============================================================== +zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/.r_rendering.log.txt')) +sink(zz) +sink(zz, type = 'message') + +#============== preparation ==================================== +# import libraries +#------------------------------------------------------------------ +# ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES +#------------------------------------------------------------------ +library('getopt') +library('rmarkdown') +library('htmltools') +#------------------------------------------------------------------ +options(stringsAsFactors = FALSE) + + +# define two helper functions +#-----: helper function 1 +#' \code{getopt_specification_matrix} returns a getopt specification matrix. +#' +#' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data. +#' 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_INSTALL_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)) { + cat('----Duplicated short flags found ----\n') + cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n') + stop('Duplicated short flags are not allowed.') + } + + # use short flags to generate long flags + 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] + ) + + as.matrix(df2) +} + +#-----: helper function 2 +#' \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 = '.') { + # 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 also include directorys, need to remove directorys + files = files[!dir.exists(files)] + 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$attribs = list('data-jstree' = '{"icon":"jstree-file"}') + li_item + }) + } + }, + { + if (length(dirs) > 0) { + lapply(dirs, function(x) { + path_end = tail(strsplit(x, '/')[[1]], 1) + # hide vakata-jstree-3.3.5 folder + if (!(path_end %in% c('vakata-jstree-3.3.5', 'rmarkdown_report_files', 'site_libs'))) { + # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2] + li_item = tags$li(path_end, file_tree(x)) + li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}') + li_item + } + }) + } + }) +} +#----------------- end of help functions ------------------------- + + +# import getopt specification matrix from a csv file +opt = getopt(getopt_specification_matrix('command-line-arguments.csv', + tool_dir = Sys.getenv('TOOL_INSTALL_DIR'))) +# 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 ========================= +# copy jstree javascript library to tool output directory +file.copy( + from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'), + to = Sys.getenv('REPORT_FILES_PATH'), + recursive = TRUE +) + +# if '_site.yml' file exists, this tool is assumed to render a website. +# otherwise, it renders a single html. +if (file.exists(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/_site.yml'))) { + # render a website + system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}') + system(command = 'cp -r ${TOOL_INSTALL_DIR}/_site.yml ${REPORT_FILES_PATH}') + render_site(input = Sys.getenv('REPORT_FILES_PATH')) +} else { + # render a single html + system(command = 'cp -r ${TOOL_INSTALL_DIR}/rmarkdown_report.Rmd ${REPORT_FILES_PATH}') + # add a few lines to 'rmarkdown_report.Rmd' to generate file tree outputs + jstree_lines = ' +## Outputs + +```{r, echo=FALSE} +tags$div(id="jstree", file_tree(Sys.getenv(\'REPORT_FILES_PATH\'))) +```' + write( + x = jstree_lines, + append = TRUE, + file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd') + ) + render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd')) +} +#=============================================================== + + +#============== expose outputs to galaxy history =============== +system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs-to-galaxy-history.sh') +#=============================================================== + + +##--------end of code rendering .Rmd templates---------------- +sink() +##=========== End of sinking output=============================