Resolved merge conflicts

Merge branch 'master' of https://github.com/Dobbs-Lab/MENTHU

# Conflicts:
#	required2.0Functions_1.R
#	server.R
#	ui.R
#	www/changelog.html

Dockerfile

@@ -17,7 +17,7 @@ RUN apt-get update && apt-get install -y \
 
 # install package dependencies for MENTHU
 #RUN R -e "install.packages(c('shiny', 'XML', 'shinyjs', 'rhandsontable', 'plyr', 'stringr', 'stringi', 'rentrez', 'rlist', 'DT', 'devtools', 'httpuv', 'httr'), repos='https://cloud.r-project.org/')" -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("Biostrings")' -e 'devtools::install_github("rstudio/shiny-incubator")'
-RUN R -e "install.packages(c('shiny', 'XML', 'xml2', 'shinyjs', 'rhandsontable', 'plyr', 'stringr', 'stringi', 'rentrez', 'rlist', 'DT', 'devtools', 'curl'), repos='https://cloud.r-project.org/')" -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("Biostrings")' -e 'devtools::install_github("rstudio/shiny-incubator")'
+RUN R -e "install.packages(c('shiny', 'XML', 'xml2', 'shinyjs', 'rhandsontable', 'plyr', 'stringr', 'stringi', 'rentrez', 'rlist', 'DT', 'devtools', 'curl', 'plyr', 'jsonlite', 'httr'), repos='https://cloud.r-project.org/')" -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("Biostrings")' -e 'devtools::install_github("rstudio/shiny-incubator")'
 
 # Copy MENTHU to image
 RUN mkdir /root/menthu/

README.md

@@ -1,10 +1,10 @@
 # MENTHU
 This is a repository for the MENTHU knockout site recommender.
 
-You can run MENTHU online through a web interface here: http://ll-g2f.gdcb.iastate.edu/menthu/
+You can run MENTHU online through a web interface here: http://genesculpt.org/menthu/
 
 
-### If you already have R and/or RStudio installed, you can jump to [here](https://github.com/Dobbs-Lab/MENTHU#run-menthu-locally) to immmediately start running MENTHU locally.
+### If you already have R and/or RStudio installed, you can jump to [here](https://github.com/Dobbs-Lab/MENTHU#3-run-menthu-locally) to immmediately start running MENTHU locally.
 
 ### If you are having issues running MENTHU locally, please check the [Troubleshooting](https://github.com/Dobbs-Lab/MENTHU#troubleshooting) section before requesting help.
 
@@ -78,25 +78,21 @@ You can copy and paste the code blocks below into your R/RStudio console to run
 
 #Install CRAN packages
 install.packages(c("shiny", "shinyjs", "Rcpp", "plyr", "stringr", "stringi", "shinyTable", 
-                   "rentrez", "rlist", "DT", "xlsx", "devtools", "rhandsontable"))
+                   "rentrez", "rlist", "DT", "xlsx", "devtools", "rhandsontable", "httr", "jsonlite", "xml2"))
 
 #Install 'Biostrings' package from Bioconductor
 source("https://bioconductor.org/biocLite.R")
 biocLite("Biostrings")
 
-#Install 'ShinyIncubator' and 'ShinyTable' from GitHub
+#Install 'ShinyIncubator' from GitHub
 devtools::install_github("rstudio/shiny-incubator", force = TRUE)
-devtools::install_github("trestletech/shinyTable",  force = TRUE)
 ```
 
 ### Run this code every time you want to use the tool, including the first time:
 
 ```
-#Load Shiny in the R/RStudio Environment
-library(shiny)
-
 #Retrieve, load, and run MENTHU from GitHub
-runGitHub("MENTHU", "Dobbs-Lab")
+shiny::runGitHub("MENTHU", "Dobbs-Lab")
 ```
 
 You're all set!

required2.0Functions_1.R

@@ -1965,7 +1965,6 @@ reverseComplement.list <- function(seq, type = "DNA"){
 	return(unlist(retList))
 }
 
-#' stripWhiteSpace
 #'
 #' This function removes all white space from character vectors. If it is passed a data frame, it will remove all white space from all columns with character data types.
 #'

server.R

@@ -11,8 +11,9 @@ library(DT)
 library(plyr)
 library(Rcpp)
 library(curl)
-library(jsonlite)
 library(httr)
+library(jsonlite)
+library(xml2)
 
 # Required supporting files
 source("apeShiftFunctions.R")
@@ -1317,7 +1318,7 @@ shinyServer(function(input, output, session){
 			# Calculate the MENTHU score
 			stuff   <<- calculateMENTHUGeneSeq(pams, cutDistances, overhangs, wiggle = TRUE, wiggleRoom = 39, 
 																				 stripWhiteSpace(input$geneSeq), exonIn, progress, talArmin, talArmax, talSpamin, talSpamax)
-			
+
 			results <<- stuff[[1]]
 
 			if(is.numeric(results)){

ui.R

@@ -13,6 +13,7 @@ shinyUI(function(request){
 
 						 #Page title box
 						 tags$div(""),
+
 
 						 ########ABOUT TAB#################################################
 						 tabPanel(#id = 'about',
@@ -781,4 +782,4 @@ shinyUI(function(request){
 	)}
 )
 
-#
+#

www/changelog.html

@@ -15,6 +15,11 @@
 <p>Issue: After submitting and getting results back, switching the input type (e.g., from GenBank to Ensembl) and then resubmitting without resetting the form results in the "Download Results" button downloading the entire page in HTM, rather than the results table in CSV.</p> 
 <p>Temporary workaround: While we implement a fix, use the "Reset Form" link in between uses for best results.</p>
 <br />
+<p><strong>2019-02-08 v2.0.8</strong></p>
+<ul>
+	<li>Fixed bug where newline characters in copy/paste input were read as part of the sequence; newline/whitespace characters in pasted sequences are now automatically removed.</li>
+</ul>
+<br />
 <p><strong>2018-10-12 v2.0.7</strong></p>
 <ul>
 	<li>Added Ensembl support</li>