Merge pull request #64 from databio/dev

fixing hg38 bug and now including commit hash
databio · Mar 20, 2018 · fb91669 · fb91669
2 parents 72f1008 + 3d581be
commit fb91669
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Showing 4 changed files with 51 additions and 23 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -17,21 +17,21 @@ before_install:
 install:
   - if [ "$TRAVIS_BRANCH" == "master" ]; then
     cd docker/ ;
-    docker build --no-cache -t databio/lolaweb:latest . ;
-    docker push databio/lolaweb:latest;
-    aws sqs send-message --queue-url 'https://queue.amazonaws.com/474683445819/lola-updates' --message-body $TRAVIS_BRANCH;
+    docker build --no-cache -t databio/lolaweb:latest . || exit 1;
+    docker push databio/lolaweb:latest || exit 1;
+    aws sqs send-message --queue-url 'https://queue.amazonaws.com/474683445819/lola-updates' --message-body $TRAVIS_BRANCH || exit 1;
     fi
   - if [ "$TRAVIS_BRANCH" == "staging" ]; then
     cd docker/staging/ ;
-    docker build --no-cache -t databio/lolaweb:staging . ;
-    docker push databio/lolaweb:staging;
-    aws sqs send-message --queue-url 'https://queue.amazonaws.com/474683445819/lola-updates' --message-body $TRAVIS_BRANCH;
+    docker build --no-cache -t databio/lolaweb:staging . || exit 1;
+    docker push databio/lolaweb:staging || exit 1;
+    aws sqs send-message --queue-url 'https://queue.amazonaws.com/474683445819/lola-updates' --message-body $TRAVIS_BRANCH || exit 1;
     fi
   - if [ "$TRAVIS_BRANCH" == "dev" ]; then
     cd docker/dev/ ;
-    docker build --no-cache -t databio/lolaweb:dev . ;
-    docker push databio/lolaweb:dev;
-    aws sqs send-message --queue-url 'https://queue.amazonaws.com/474683445819/lola-updates' --message-body $TRAVIS_BRANCH;
+    docker build --no-cache -t databio/lolaweb:dev . || exit 1;
+    docker push databio/lolaweb:dev || exit 1;
+    aws sqs send-message --queue-url 'https://queue.amazonaws.com/474683445819/lola-updates' --message-body $TRAVIS_BRANCH || exit 1;
     fi
 
 notifications:

diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@ This repository contains two components: 1) the shiny [app source code](apps/LOL
 
 ## Shiny app
 
-LOLAweb is implemented as an interactive shiny app. You can run this app locally by following the [instructions in the appfolder](apps/LOLAweb/).
+LOLAweb is implemented as an interactive Shiny app. You can run this app locally by following the [instructions in the appfolder](apps/LOLAweb/).
 
 ## Dockerfile
 

diff --git a/apps/LOLAweb/app.R b/apps/LOLAweb/app.R
@@ -15,6 +15,8 @@ library(GenomicDistributions)
 
 setCacheDir("cache")
 
+# get lolaweb version
+lw_version <- system(command = "git rev-parse HEAD | cut -c1-9", intern = TRUE)
 
 ui <- list( 
 
@@ -90,7 +92,7 @@ ui <- list(
                actionButton("run",
                             "RUN LOLA", 
                             class = "runLOLA"),
-               HTML("<div style='padding-top:15px; padding-left:5px;'><a href = '?key=UDYOXT3MC1E2VF7'>Sample Results</a></div>")
+               HTML("<div style='padding-top:15px; padding-left:5px;'><a href = '?key=C5SQHB6RAM12EZF'>Sample Results</a></div>")
         ),
       class = "headerBox"),
   fluidRow(
@@ -100,7 +102,7 @@ ui <- list(
            htmlOutput("messages"))
   )),
   tabPanel("Results",
-        fluidRow(div(HTML("<div class='alert alert-warning'><strong>Results</strong> is currently empty.<br>To generate result output, visit <strong>Run</strong> or view <a href = '?key=UDYOXT3MC1E2VF7'>sample results</a>.</div>"), id = "noresultsmsg")
+        fluidRow(div(HTML("<div class='alert alert-warning'><strong>Results</strong> is currently empty.<br>To generate result output, visit <strong>Run</strong> or view <a href = '?key=C5SQHB6RAM12EZF'>sample results</a>.</div>"), id = "noresultsmsg")
              ),
         fluidRow(
         column(2,
@@ -120,7 +122,7 @@ ui <- list(
                uiOutput("select_userset"),
                conditionalPanel(condition = "output.res",
                                 h4("Run Summary"),
-                                tableOutput("run_sum"))
+                                tableOutput("run_sum"), style = "font-size:10px;")
           ),
         column(10,
                tags$h4(htmlOutput("link")),
@@ -173,7 +175,11 @@ ui <- list(
   tabPanel("About",
     includeHTML("about.html")
   ),
-  footer = div(HTML("<div>Powered by <a href = 'https://somrc.virginia.edu' target ='blank'>SOMRC</a><br>A Project of the <a href ='http://databio.org/' target = 'blank'>Sheffield Lab</a><br>Source code on <a href ='https://github.com/databio/LOLAweb' target = 'blank'>Github</a><br>Try it yourself with <a href='https://github.com/databio/LOLAweb/blob/master/docker/README.md' target = 'blank'>Docker</a></div>"), align = "right", style = " bottom:0; width:100%; height:10px; padding: 10px; padding-bottom:20px; z-index: 1000;"),
+  footer = div(HTML(
+    paste0("<div>Powered by <a href = 'https://somrc.virginia.edu' target ='blank'>SOMRC</a><br>A Project of the <a href ='http://databio.org/' target = 'blank'>Sheffield Lab</a><br>Source code on <a href ='https://github.com/databio/LOLAweb' target = 'blank'>Github</a><br>Try it yourself with <a href='https://github.com/databio/LOLAweb/blob/master/docker/README.md' target = 'blank'>Docker</a>", 
+           "<br>LOLAweb commit <a href ='https://github.com/databio/lolaweb/commit/", lw_version, "'>", lw_version, "</a></div>")
+    ), 
+    align = "right", style = " bottom:0; width:100%; height:10px; padding: 10px; padding-bottom:20px; z-index: 1000;"),
   id = "mainmenu"
 )
 )
@@ -416,22 +422,26 @@ server <- function(input, output, session) {
 
         if(input$checkbox) {
 
-          userUniverse = read.table(file = input$useruniverse$datapath, header = F)
+          # userUniverse = read.table(file = input$useruniverse$datapath, header = F)
+          userUniverse = readBed(file = input$useruniverse$datapath)
+
 
           universename <- input$useruniverse$datapath
 
         } else {
 
           datapath <- paste0("universes/", input$refgenome, "/", input$defaultuniverse)
 
-          userUniverse = read.table(file = datapath, header = F)
+          # userUniverse = read.table(file = datapath, header = F)
+          userUniverse = readBed(file = datapath)
+
 
           universename <- input$defaultuniverse
 
         }
-        colnames(userUniverse) <- c('chr','start','end','id','score','strand')
-        userUniverse <- with(userUniverse, GRanges(chr, IRanges(start+1, end), strand, score, id=id))
-
+        # colnames(userUniverse) <- c('chr','start','end','id','score','strand')
+        # userUniverse <- with(userUniverse, GRanges(chr, IRanges(start+1, end), strand, score, id=id))
+        
         userSetsRedefined =	redefineUserSets(userSets, userUniverse)
 
         # load region data for each reference genome
@@ -472,7 +482,8 @@ server <- function(input, output, session) {
           query_set = paste(gsub(".bed","",unique(resRedefined$userSet)), collapse = "\n"),
           genome = input$refgenome,
           universe = gsub(".bed", "", universename),
-          region_db = input$loladb
+          region_db = input$loladb,
+          commit = lw_version
           )
 
         # create named list of multiple objects for plotting
@@ -718,7 +729,8 @@ server <- function(input, output, session) {
         "Regions ",
         "Genome ",
         "Universe ",
-        "Database "),
+        "Database ",
+        "Commit "),
       y = 
         c(as.character(rawdat_res$run_sum$start_time),
           as.character(rawdat_res$run_sum$end_time),
@@ -727,7 +739,8 @@ server <- function(input, output, session) {
           as.character(rawdat_res$run_sum$query_set),
           as.character(rawdat_res$run_sum$genome),
           as.character(rawdat_res$run_sum$universe),
-          as.character(rawdat_res$run_sum$region_db)
+          as.character(rawdat_res$run_sum$region_db),
+          as.character(rawdat_res$run_sum$commit)
         )
     , stringsAsFactors = FALSE)
 

diff --git a/apps/LOLAweb/scratch.R b/apps/LOLAweb/scratch.R
@@ -7,10 +7,11 @@ source("themes.R")
 
 dbPath = system.file("extdata", "hg19", package="LOLA")
 regionDB = loadRegionDB(dbLocation=dbPath)
+
 data("sample_universe", package="LOLA")
 # data("sample_input", package="LOLA")
 
-userSet = read.table(file = "lola_vignette_data/setB_complete.bed", header = F) 
+userSet = read.table(file = "lola_vignette_data/setB_100.bed", header = F) 
 colnames(userSet) <- c('chr','start','end','id','score','strand')
 userSet <- with(userSet, GRanges(chr, IRanges(start+1, end), strand, score, id=id))
 userSetsRedefined =	redefineUserSets(userSet, userUniverse)
@@ -264,4 +265,18 @@ x <- system.time({
   rnorm(1000000)
 })
 
+
+userSet = readBed(file = "lola_vignette_data/setB_100.bed") 
+dbPath = "reference/Core/hg38/"
+regionDB = loadRegionDB(dbLocation=dbPath)
+
+userUniverse = readBed("universes/hg38/tiles.hg38.5000.bed")
+userUniverse = read.table(file = "universes/hg38/tiles.hg38.5000.bed", header = F) 
+colnames(userUniverse) <- c('chr','start','end','id','score','strand')
+userUniverse <- with(userUniverse, GRanges(chr, IRanges(start+1, end), strand, score, id=id))
+
+userSetsRedefined =	redefineUserSets(userSet, userUniverse)
+
+
+resRedefined = runLOLA(userSetsRedefined, userUniverse, regionDB, cores=1)