diff --git a/R/helper_functions.R b/R/helper_functions.R
index d15e5a14e9f732ea083f19b07668f16c161932cd..d94bc7b10998a3618322599d31b1717f9eda0929 100644
--- a/R/helper_functions.R
+++ b/R/helper_functions.R
@@ -15,6 +15,45 @@ getPackagesWithTitle <- function() {
}
+getWorkflows <- function() {
+
+ data <- allWORKFLOWS
+
+ size <- 0
+
+ for (tools in data) {
+ if(length(tools$install) > 0) {
+ size <- size + 1
+ }
+ }
+
+ Tool <- character(size)
+ Version <- character(size)
+ Author <- character(size)
+ Description <- character(size)
+ Link <- character(size)
+
+ i=1
+ for (tools in data) {
+ Tool[i] = tools$name
+ Version[i] = tools$version
+ Author[i] = tools$author
+ Description[i] = tools$description
+ Link[i] = paste0("<a href='", tools$documentation, "'>documentation</a>")
+ i = i + 1
+ }
+
+
+ result <- data.frame(Workflow=Tool,
+ Version=Version,
+ Author=Author,
+ Description=Description,
+ Link=Link)
+
+ return(result)
+
+
+}
getBioconductorPackage <- function() {
@@ -61,6 +100,38 @@ getBioconductorPackage <- function() {
return(result)
}
+getInstallToolPackageWorkflow <- function(tool, containerType) {
+
+ data <- allWORKFLOWS
+
+ size <- length(data)
+
+ intalls <- ""
+ res <- ""
+
+ for (tools in data) {
+ splitB <- strsplit(tool, "%")
+ name <- splitB[[1]][1]
+ version <- splitB[[1]][2]
+
+ if(tools$name == name) {
+ if(tools$version == version) {
+ for (c in tools$dependencies) {
+ tt <- paste0(c$name, "%", c$version)
+ print(tt)
+ res <- paste0(res, getInstallToolPackageBioContainer(tt, containerType))
+ res <- paste0(res, "\n")
+ }
+ res <- paste0(res, "\t", tools$install, collapse='\n' )
+ return(res)
+ }
+ }
+ }
+
+ return("\t")
+
+}
+
getInstallToolPackageBioContainer <- function(tool, containerType) {
data <- allBIOCONTAINER
@@ -76,6 +147,9 @@ getInstallToolPackageBioContainer <- function(tool, containerType) {
if(tools$name == name) {
if(tools$version == version) {
+
+
+
res <- paste0("\t", tools$install, collapse='\n' )
return(res)
}
@@ -113,5 +187,33 @@ getInstallToolEnvBioContainer <- function(tool, containerType) {
return (FALSE)
}
+getInstallToolEnvWorkflows <- function(tool, containerType) {
+
+ data <- allWORKFLOWS
+
+ size <- length(data)
+
+ intalls <- ""
+
+ for (tools in data) {
+ splitB <- strsplit(tool, "%")
+ name <- splitB[[1]][1]
+ version <- splitB[[1]][2]
+
+ if(tools$name == name) {
+ if(tools$version == version) {
+ if(is.null(tools$env)) {
+ return (FALSE)
+ } else {
+ return(tools$env)
+ }
+ }
+ }
+ }
+
+ return (FALSE)
+}
+
+
diff --git a/app.R b/app.R
index 1beba587877f94760c610d14a7c05d09f692bc26..6bebe07bd52d2cf3ebb4bdbd00afb27732d6a24b 100644
--- a/app.R
+++ b/app.R
@@ -65,6 +65,20 @@ server <- function( input, output, session) {
i = i + 1
}
+ allWORKFLOWS <<- list()
+ TMP <<- yaml.load_file("workflow.yaml")$workflows
+ i = 1
+ j = 1
+ allWORKFLOWS <<- list()
+ for(x in TMP) {
+ if(length(TMP[[i]]$install) > 0) {
+
+ allWORKFLOWS[[j]] <<- TMP[[i]]
+ j = j + 1
+ }
+ i = i + 1
+ }
+
hide("downloadContainerFile")
source("./server/opt_home.R", local=TRUE)
diff --git a/pages/pages_def_home.R b/pages/pages_def_home.R
index f71c8de3bcfd052a7b43517fd47ad87d47d7da35..266135fcc869de1e0009488992a111670de44b4d 100755
--- a/pages/pages_def_home.R
+++ b/pages/pages_def_home.R
@@ -91,7 +91,14 @@ tabHome = fluidPage(align="left",
selectizeInput('rgithubpackagelist', 'R Github selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
br(), br(),
- DT::dataTableOutput('dtrgithubpackage')))
+ DT::dataTableOutput('dtrgithubpackage'))),
+
+ tabPanel('Workflows',
+ div(id = "formWorkflows",
+ br(),
+ selectizeInput('selectedWorkflows', 'Workflows selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000))),
+
+ DT::dataTableOutput('dtWorkflows'))
)
)
diff --git a/server/opt_home.R b/server/opt_home.R
index afcd5e2db1862667a6cf0d2d708e5456a881ea10..9a0234615413bb137f0867533d63bc940cf8efc2 100755
--- a/server/opt_home.R
+++ b/server/opt_home.R
@@ -31,6 +31,19 @@ output$dtbiocontainer <- DT::renderDataTable({
return(result)
}, filter='top', escape = FALSE, rownames= FALSE,server = TRUE)
+getWorkflows
+
+output$dtWorkflows <- DT::renderDataTable({
+ result <- data.frame(Workflow=character(),
+ Author=character(),
+ Version=character(),
+ Description=character())
+
+ result <- getWorkflows()
+
+
+ return(result)
+}, filter='top', escape = FALSE, rownames= FALSE,server = TRUE)
createHeader <- function() {
@@ -76,7 +89,10 @@ createEnv <- function(result) {
result <- paste(result, "\texport R_CONFIG_DIR", sep = "\n")
}
+
+ haveB <- FALSE
if(!is.null(input$dtbiocontainer_rows_all)) {
+ haveB <- TRUE
result <- paste(result, "\texport PATH=/opt/conda/bin:$PATH", sep = "\n")
result <- paste(result, "\texport PATH=/opt/biotools/bin:$PATH", sep = "\n")
result <- paste(result, "\texport ROOTSYS=/opt/biotools/root", sep = "\n")
@@ -85,6 +101,18 @@ createEnv <- function(result) {
result <- createPathBiocontainer(result)
}
+ if(!is.null(input$dtWorkflows_rows_all)) {
+ if(!haveB) {
+ result <- paste(result, "\texport PATH=/opt/conda/bin:$PATH", sep = "\n")
+ result <- paste(result, "\texport PATH=/opt/biotools/bin:$PATH", sep = "\n")
+ result <- paste(result, "\texport ROOTSYS=/opt/biotools/root", sep = "\n")
+ result <- paste(result, "\texport LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'", sep = "\n")
+ }
+
+ result <- paste(result, "\texport PATH=/opt/workflows/bin:$PATH", sep = "\n")
+ result <- createPathWorkflow(result)
+ }
+
} else {
if(input$rtemplate == "none" || input$fromTemplate == "r-base") {
@@ -102,7 +130,9 @@ createEnv <- function(result) {
result <- paste(result, "RUN export R_CONFIG_DIR", sep = "\n")
}
+ haveB <- FALSE
if(!is.null(input$dtbiocontainer_rows_all)) {
+ haveB <- TRUE
result <- paste(result, "RUN export PATH=/opt/conda/bin:$PATH", sep = "\n")
result <- paste(result, "RUN export PATH=/opt/biotools/bin:$PATH", sep = "\n")
result <- paste(result, "RUN export ROOTSYS=/opt/biotools/root", sep = "\n")
@@ -110,6 +140,17 @@ createEnv <- function(result) {
result <- createPathBiocontainer(result)
}
+
+ if(!is.null(input$dtWorkflows_rows_all)) {
+ if(!haveB) {
+ result <- paste(result, "RUN export PATH=/opt/conda/bin:$PATH", sep = "\n")
+ result <- paste(result, "RUN export PATH=/opt/biotools/bin:$PATH", sep = "\n")
+ result <- paste(result, "RUN export ROOTSYS=/opt/biotools/root", sep = "\n")
+ result <- paste(result, "RUN export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'", sep = "\n")
+ }
+ result <- paste(result, "RUN export PATH=/opt/workflows/bin:$PATH", sep = "\n")
+ result <- createPathWorkflow(result)
+ }
}
result <- paste0(result, "\n")
@@ -355,6 +396,40 @@ createBioconductorPackage <- function(result) {
return(result)
}
+
+createPathWorkflow <- function(result) {
+
+ if(input$containerType == "singularity") {
+ selectBioTool <- input$selectedWorkflows
+ for (tool in selectBioTool){
+
+ to <- getInstallToolEnvWorkflows(tool, input$containerType)
+
+ if(is.character(to)) {
+ result <- paste0(result, "\n\t", to)
+ }
+
+ }
+
+ } else {
+ selectBioTool <- input$selectedWorkflows
+ for (tool in selectBioTool){
+
+ to <- getInstallToolEnvWorkflows(tool, input$containerType)
+
+ if(is.character(to)) {
+ result <- paste0(result, "\nRUN ", to)
+ }
+
+ }
+
+ }
+
+ return(result)
+
+}
+
+
createPathBiocontainer <- function(result) {
if(input$containerType == "singularity") {
@@ -385,6 +460,132 @@ createPathBiocontainer <- function(result) {
return(result)
+}
+#' Use for create Workflows content
+createWorkflows <- function(result, haveR, haveConda) {
+
+ if(input$containerType == "singularity") {
+ selectWorkflows <- input$selectedWorkflows
+
+ result <- paste0(result, "\n")
+
+ if(!haveConda) {
+
+ result <- paste(result, "\tapt-get install -y autotools-dev automake cmake curl grep sed dpkg fuse git zip openjdk-8-jre build-essential pkg-config python python-dev python-pip bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev libncurses5-dev libncursesw5-dev", sep = "\n")
+ result <- paste(result, "\tapt-get update", sep = "\n")
+
+ result <- paste0(result, "\n")
+
+ result <- paste(result, "\techo \'export PATH=/opt/conda/bin:$PATH\' > /etc/profile.d/conda.sh && \\",
+ "\twget --quiet https://repo.continuum.io/miniconda/Miniconda2-4.0.5-Linux-x86_64.sh -O ~/miniconda.sh && \\",
+ "\t/bin/bash ~/miniconda.sh -b -p /opt/conda && \\",
+ "\trm ~/miniconda.sh", sep = "\n")
+
+ result <- paste0(result, "\n")
+
+ result <- paste(result, "\tTINI_VERSION=`curl https://github.com/krallin/tini/releases/latest | grep -o \"/v.*\\\"\" | sed \'s:^..\\(.*\\).$:\\1:\'` && \\",
+ "\tcurl -L \"https://github.com/krallin/tini/releases/download/v${TINI_VERSION}/tini_${TINI_VERSION}.deb\" > tini.deb && \\",
+ "\tdpkg -i tini.deb && \\",
+ "\trm tini.deb && \\",
+ "\tapt-get clean", sep = "\n")
+
+ result <- paste0(result, "\n")
+
+ result <- paste(result, '\tif [ ! -d "/opt/biotools" ];then mkdir /opt/biotools; fi', sep = "\n")
+ result <- paste(result, '\tif [ ! -d "/opt/biotools/bin" ];then mkdir /opt/biotools/bin; fi', sep = "\n")
+ result <- paste(result, "\tchmod 777 -R /opt/biotools/", sep = "\n")
+ result <- paste(result, "\texport PATH=/opt/biotools/bin:$PATH", sep = "\n")
+
+ result <- paste(result, "\tchmod 777 -R /opt/conda/", sep = "\n")
+ result <- paste(result, "\texport PATH=/opt/conda/bin:$PATH", sep = "\n")
+
+ if(!haveR) {
+ result <- paste(result, "\tconda config --add channels r", sep = "\n")
+ }
+
+ result <- paste(result, "\tconda config --add channels bioconda", sep = "\n")
+ result <- paste(result, "\tconda upgrade conda", sep = "\n")
+
+ result <- paste0(result, "\n")
+
+ }
+
+ result <- paste(result, '\tif [ ! -d "/opt/workflows" ];then mkdir /opt/workflows; fi', sep = "\n")
+ result <- paste(result, '\tif [ ! -d "/opt/workflows/bin" ];then mkdir /opt/workflows/bin; fi', sep = "\n")
+ result <- paste(result, "\tchmod 777 -R /opt/workflows/", sep = "\n")
+ result <- paste(result, "\texport PATH=/opt/workflows/bin:$PATH", sep = "\n")
+
+ for (tool in selectWorkflows){
+
+ result <- paste(result, '############### Install Workflow tools ##############', sep = "\n")
+
+
+ result <- paste(result, getInstallToolPackageWorkflow(tool, input$containerType), sep="\n\n")
+ }
+ } else {
+ selectBioTool <- input$selectedBiocontainer
+
+ result <- paste0(result, "\n")
+
+ if(!haveConda) {
+
+ result <- paste(result, "RUN apt-get install -y autotools-dev automake cmake curl grep sed dpkg fuse git zip openjdk-8-jre build-essential pkg-config python python-dev python-pip bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev libncurses5-dev libncursesw5-dev", sep = "\n")
+ result <- paste(result, "RUN apt-get update", sep = "\n")
+
+ result <- paste0(result, "\n")
+
+ result <- paste(result, "RUN echo \'export PATH=/opt/conda/bin:$PATH\' > /etc/profile.d/conda.sh && \\",
+ "\twget --quiet https://repo.continuum.io/miniconda/Miniconda2-4.0.5-Linux-x86_64.sh -O ~/miniconda.sh && \\",
+ "\t/bin/bash ~/miniconda.sh -b -p /opt/conda && \\",
+ "\trm ~/miniconda.sh", sep = "\n")
+
+ result <- paste0(result, "\n")
+
+ result <- paste(result, "RUN TINI_VERSION=`curl https://github.com/krallin/tini/releases/latest | grep -o \"/v.*\\\"\" | sed \'s:^..\\(.*\\).$:\\1:\'` && \\",
+ "\tcurl -L \"https://github.com/krallin/tini/releases/download/v${TINI_VERSION}/tini_${TINI_VERSION}.deb\" > tini.deb && \\",
+ "\tdpkg -i tini.deb && \\",
+ "\trm tini.deb && \\",
+ "\tapt-get clean", sep = "\n")
+
+ result <- paste0(result, "\n")
+
+ result <- paste(result, "RUN mkdir /opt/biotools", sep = "\n")
+ result <- paste(result, "RUN mkdir /opt/biotools/bin", sep = "\n")
+ result <- paste(result, "RUN chmod 777 -R /opt/biotools/", sep = "\n")
+ result <- paste(result, "ENV PATH=/opt/biotools/bin:${PATH}", sep = "\n")
+
+ result <- paste(result, "RUN chmod 777 -R /opt/conda/", sep = "\n")
+ result <- paste(result, "ENV PATH=/opt/conda/bin:${PATH}", sep = "\n")
+
+ if(!haveR) {
+ result <- paste(result, "RUN conda config --add channels r", sep = "\n")
+ }
+
+ result <- paste(result, "RUN conda config --add channels bioconda", sep = "\n")
+ result <- paste(result, "RUN conda upgrade conda", sep = "\n")
+
+ result <- paste0(result, "\n")
+
+ }
+
+ result <- paste(result, "RUN mkdir /opt/workflows", sep = "\n")
+ result <- paste(result, "RUN mkdir /opt/workflows/bin", sep = "\n")
+ result <- paste(result, "RUN chmod 777 -R /opt/workflows/", sep = "\n")
+ result <- paste(result, "ENV PATH=/opt/workflows/bin:${PATH}", sep = "\n")
+
+ for (tool in selectBioTool){
+
+ result <- paste(result, '############### Install Workflow ##############', sep = "\n")
+
+
+ result <- paste0(result, "\nRUN ", getInstallToolPackageWorkflow(tool, input$containerType))
+ }
+
+ }
+
+ result <- paste0(result, "\n")
+ return(result)
+
}
#' Use for create Biocontainer content
@@ -530,10 +731,14 @@ createContentFile <- function() {
result <- createBioconductorPackage(result)
result <- createGithubPackage(result)
+ haveBiocontainer <- FALSE
if(!is.null(input$selectedBiocontainer)) {
+ haveBiocontainer <- TRUE
result <- createBiocontainer(result, haveR)
}
+ result <- createWorkflows(result, haveR, haveBiocontainer)
+
result <- createExect(result)
result <- paste(result, input$customDataContainer, sep = "\t\n")
@@ -605,6 +810,25 @@ observe({
})
+
+
+observe({
+
+ if(is.null(input$dtWorkflows_rows_selected)) {
+ shinyjs::reset("formWorkflows")
+ } else {
+ i = 1
+ selectWorkflows <- list()
+ for(x in input$dtWorkflows_rows_selected) {
+ selectWorkflows[i] = paste(allWORKFLOWS[[x]]$name, allWORKFLOWS[[x]]$version, sep = "%")
+ i = i + 1
+ }
+ selectWorkflows <- c(unlist(selectWorkflows))
+ updateSelectizeInput(session,"selectedWorkflows", choices = selectWorkflows, selected = selectWorkflows, options = list())
+ }
+})
+
+
observe({
if(is.null(input$dtrcranpackage_rows_selected)) {