From fef81172c5afee50f9b50386ee033c4cc9648a3b Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Tue, 9 Nov 2021 08:41:19 +0100
Subject: [PATCH] singularity def is generated from docker def
---
R/menugauche.R | 28 ++-
pages/pages_def_home.R | 33 +--
server/opt_home.R | 486 ++++++++++-------------------------------
3 files changed, 141 insertions(+), 406 deletions(-)
diff --git a/R/menugauche.R b/R/menugauche.R
index d5412ab..899ba01 100644
--- a/R/menugauche.R
+++ b/R/menugauche.R
@@ -1,11 +1,23 @@
library("shinydashboard")
MenuGauche = sidebarMenu(id = "sidebarmenu",
- menuItem("Home", tabName = "Home", icon = icon("home", lib="font-awesome")),
-
- tags$br(), tags$br(), tags$br(),
-
- menuItem("Team", icon = icon("book", lib="font-awesome"),
- menuItem("Jimmy Lopez", href = "http://www.isem.univ-montp2.fr/recherche/les-plate-formes/bioinformatique-labex/personnel/", newtab = TRUE, icon = shiny::icon("male"), selected = NULL )
- )
-
+ menuItem("Home", tabName = "Home", icon = icon("home", lib="font-awesome")),
+ br(),
+ textInput("imageName", "Image Name", ""),
+
+ selectizeInput('fromTemplate', 'From:', choices = c(`ubuntu:16.04` = 'ubuntu:16.04', `ubuntu:18.04` = 'ubuntu:18.04', `ubuntu:20.04` = 'ubuntu:20.04'), selected = "ubuntu:20.04", multiple = FALSE),
+
+ radioButtons("containerType", "Container type:", choices = list("Singularity" = "singularity", "Docker" = "docker"), selected = "singularity"),
+ br(),
+ #selectizeInput('rcranpackagelist', 'R CRAN:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
+ selectizeInput('rtemplate', 'R origin:', choices = c(`None` = 'none', `R from source 3.4.3` = 'source', `R from source 3.4.4` = 'source2', `R from source 3.5.0` = 'source3', `R from source 3.6.0` = 'source4', `R from source 4.0.1` = 'source5', `R from r-base` = 'base', `R from CRAN depo` = 'cran'), selected = "none", multiple = FALSE),
+ #selectizeInput('biocontainers', 'BioContainers tools :', choices = getBioconductorPackage(), multiple = TRUE),
+
+ textAreaInput("customDataContainer", "Add custom line to container file:"),
+ br(),
+ actionButton("createContainer", label = "Generate", icon("paper-plane"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
+ downloadButton('downloadContainerFile', label = "Dowload", style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
+ br(),br(), br(),
+ menuItem("Team", icon = icon("book", lib="font-awesome"),
+ menuItem("Jimmy Lopez", href = "http://www.isem.univ-montp2.fr/recherche/les-plate-formes/bioinformatique-labex/personnel/", newtab = TRUE, icon = shiny::icon("male"), selected = NULL )
+ )
)
diff --git a/pages/pages_def_home.R b/pages/pages_def_home.R
index 08ea62c..2a8c69d 100755
--- a/pages/pages_def_home.R
+++ b/pages/pages_def_home.R
@@ -5,6 +5,7 @@ tabHome = fluidPage(align="left",
title = "Help",
width = NULL,
collapsible = TRUE,
+ collapsed = T,
status="primary",
solidHeader = TRUE,
tags$b("Bioinformatics tools: "),
@@ -23,36 +24,8 @@ tabHome = fluidPage(align="left",
p("singularity exec ubuntu6.10_stacks2.0.simg python -c 'import pysam; print 2*2'")
)),
- column(width = 2,
- box(
- title = "Params",
- width = NULL,
- collapsible = TRUE,
- solidHeader = TRUE,
- status="primary",
-
- textInput("imageName", "Image Name", ""),
- br(),
- #selectizeInput('fromTemplate', 'From:', choices = c(`ubuntu:16.04` = 'ubuntu:16.04', `r-base` = 'r-base'), selected = "r-base", multiple = FALSE),
- selectizeInput('fromTemplate', 'From:', choices = c(`ubuntu:16.04` = 'ubuntu:16.04', `ubuntu:18.04` = 'ubuntu:18.04', `ubuntu:20.04` = 'ubuntu:20.04'), selected = "ubuntu:20.04", multiple = FALSE),
-
- br(),
- radioButtons("containerType", "Container type:", choices = list("Singularity" = "singularity", "Docker" = "docker"), selected = "singularity"),
- br(),
- #selectizeInput('rcranpackagelist', 'R CRAN:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
- selectizeInput('rtemplate', 'R origin:', choices = c(`None` = 'none', `R from source 3.4.3` = 'source', `R from source 3.4.4` = 'source2', `R from source 3.5.0` = 'source3', `R from source 3.6.0` = 'source4', `R from source 4.0.1` = 'source5', `R from r-base` = 'base', `R from CRAN depo` = 'cran'), selected = "none", multiple = FALSE),
- #selectizeInput('biocontainers', 'BioContainers tools :', choices = getBioconductorPackage(), multiple = TRUE),
-
-
-
- textAreaInput("customDataContainer", "Add custom line to container file:"),
- br(), br(),
-
- actionButton("createContainer", label = "Generate", icon("paper-plane"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
- downloadButton('downloadContainerFile', label = "Dowload", style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
-
- )),
- column(width = 10,
+
+ column(width = 12,
box(
id = "boxPackage",
title = "Packages and tools",
diff --git a/server/opt_home.R b/server/opt_home.R
index 17e61f4..ea42ba9 100755
--- a/server/opt_home.R
+++ b/server/opt_home.R
@@ -51,23 +51,17 @@ output$dtWorkflows <- DT::renderDataTable({
createHeader <- function() {
-
result <- ""
-
- if(input$containerType == "singularity") {
- result <- "Bootstrap: docker"
- result <- paste0(result, "\nFrom: ", input$fromTemplate)
- result <- paste(result, "IncludeCmd: yes", sep = "\n")
- } else { # else docker
- result <- paste0("FROM ", input$fromTemplate)
- }
-
+ result <- paste0("FROM ", input$fromTemplate)
result <- paste0(result, "\n")
return(result)
}
createEnv <- function(result) {
-
+ result <- paste(result, "ARG DEBIAN_FRONTEND=noninteractive","ARG TZ=Europe/Paris", sep="\n")
+ result <- paste(result, "export DEBIAN_FRONTEND=noninteractive","export TZ=Europe/Paris", sep="\n")#for singularity
+
+ result <- paste0(result, "\n")
Rversion = "3.4.3"
if(input$rtemplate == "source2") {
Rversion = "3.4.4"
@@ -79,87 +73,49 @@ createEnv <- function(result) {
Rversion = "4.0.1"
}
- if(input$containerType == "singularity") {
- result <- paste(result, "%environment", sep = "\n")
-
- if(input$rtemplate == "none" || input$fromTemplate == "r-base") {
-
- } else if(input$rtemplate == "base") {
- result <- paste(result, "\tR_VERSION=3.2.5", sep = "\n")
- result <- paste(result, "\texport R_VERSION", sep = "\n")
- result <- paste(result, "\tR_CONFIG_DIR=/etc/R/", sep = "\n")
- result <- paste(result, "\texport R_CONFIG_DIR", sep = "\n")
- } else {
-
- result <- paste0(result, "\n\tR_VERSION=", Rversion)
- result <- paste(result, "\texport R_VERSION", sep = "\n")
- result <- paste(result, "\tR_CONFIG_DIR=/etc/R/", sep = "\n")
- 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:$PATH", sep = "\n")
- result <- paste(result, "\texport ROOTSYS=/opt/biotools/root", sep = "\n")
- result <- paste(result, "\texport LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'", sep = "\n")
-
- result <- createPathBiocontainer(result)
- }
-
- if(!is.null(input$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")
- }
+ selectCRAN <- input$selectedCRAN
+ sizeCRAN <- length(selectCRAN)
+ selectBIO <- input$selectedConductor
+ sizeBIO <- length(selectBIO)
+ selectGithub <- input$rgithubpackagelist
+ sizeGITHUB <- length(selectGithub)
- result <- paste(result, "\texport PATH=/opt/workflows/bin:$PATH", sep = "\n")
- result <- createPathWorkflow(result)
- }
-
-
+ if(input$rtemplate == "none" & sizeCRAN == 0 & sizeBIO == 0 & sizeGITHUB == 0) {
+
+ } else if(input$rtemplate == "base") {
+ result <- paste0(result, "ENV R_VERSION=", Rversion)
+ #result <- paste(result, "RUN export R_VERSION", sep = "\n")
+ result <- paste(result, "ENV R_CONFIG_DIR=/etc/R/", sep = "\n")
+ result <- paste(result, "RUN export R_CONFIG_DIR", sep = "\n")
+
} else {
- if(input$rtemplate == "none" || input$fromTemplate == "r-base") {
-
- } else if(input$rtemplate == "base") {
- result <- paste0(result, "ENV R_VERSION=", Rversion)
- result <- paste(result, "RUN export R_VERSION", sep = "\n")
- result <- paste(result, "ENV R_CONFIG_DIR=/etc/R/", sep = "\n")
- result <- paste(result, "RUN export R_CONFIG_DIR", sep = "\n")
-
- } else {
- result <- paste(result, "ENV R_VERSION=3.4.3", sep = "\n")
- result <- paste(result, "RUN export R_VERSION", sep = "\n")
- result <- paste(result, "ENV R_CONFIG_DIR=/etc/R/", sep = "\n")
- result <- paste(result, "RUN export R_CONFIG_DIR", sep = "\n")
- }
-
- haveB <- FALSE
- if(!is.null(input$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")
- result <- paste(result, "RUN export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'", sep = "\n")
-
- result <- createPathBiocontainer(result)
- }
+ result <- paste(result, "ENV R_VERSION=3.4.3", sep = "\n")
+ #result <- paste(result, "RUN export R_VERSION", sep = "\n")
+ result <- paste(result, "ENV R_CONFIG_DIR=/etc/R/", sep = "\n")
+ 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:$PATH", sep = "\n")
+ result <- paste(result, "RUN export ROOTSYS=/opt/biotools/root", sep = "\n")
+ result <- paste(result, "RUN export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'", sep = "\n")
- if(!is.null(input$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:$PATH", sep = "\n")
- result <- createPathWorkflow(result)
- }
+ result <- createPathBiocontainer(result)
+ }
+ if(!is.null(input$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:$PATH", sep = "\n")
+ result <- createPathWorkflow(result)
}
+
result <- paste0(result, "\n")
return(result)
@@ -167,59 +123,36 @@ createEnv <- function(result) {
createLabel <- function(result) {
- if(input$containerType == "singularity") {
- result <- paste(result, "%labels", sep = "\n")
- result <- paste(result, "\tAuthor YourName", sep = "\n")
- result <- paste(result, "\tVersion v0.0.1", sep = "\n")
- result <- paste0(result, "\n\tbuild_date ", format(Sys.time(), "%Y %b %d"))
- } else {
result <- paste(result, "LABEL Author YourName", sep = "\n")
result <- paste(result, "LABEL Version v0.0.1", sep = "\n")
result <- paste0(result, "\n", "LABEL build_date ", format(Sys.time(), "%Y %b %d"))
- }
result <- paste0(result, "\n")
return(result)
}
createExect <- function(result) {
-
- if(input$containerType == "singularity") {
- result <- paste(result, "%apprun run", sep = "\n")
- result <- paste(result, '\texec /bin/bash "$@"', sep = "\n")
- result <- paste0(result, "\n")
- result <- paste(result, "%runscript", sep = "\n")
- result <- paste(result, '\texec /bin/bash "$@"', sep = "\n")
- } else {
- result <- paste(result, "CMD exec /bin/bash \"$@\"", sep = "\n")
- }
-
+
+ result <- paste(result, "CMD exec /bin/bash \"$@\"", sep = "\n")
result <- paste0(result, "\n")
return(result)
}
createLibPrePost <- function(result) {
- if(input$containerType == "singularity") {
- result <- paste(result, "%post", sep = "\n")
- result <- paste(result, "\tapt-get update", sep = "\n")
- result <- paste(result, "\tapt-get install -y wget libblas3 libblas-dev liblapack-dev liblapack3 curl", sep = "\n")
- result <- paste(result, "\tapt-get install -y gcc fort77 aptitude", sep = "\n")
- result <- paste(result, "\taptitude install -y g++ xorg-dev libreadline-dev gfortran", sep = "\n")
- result <- paste(result, "\tapt-get install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev git", sep = "\n")
- result <- paste(result, "\tapt-get update", sep = "\n")
- } else {
result <- paste(result, "RUN apt-get update", sep = "\n")
+
result <- paste(result, "RUN apt-get install -y wget libblas3 libblas-dev liblapack-dev liblapack3 curl", sep = "\n")
result <- paste(result, "RUN apt-get install -y gcc fort77 aptitude", sep = "\n")
result <- paste(result, "RUN aptitude install -y g++ xorg-dev libreadline-dev gfortran", sep = "\n")
result <- paste(result, "RUN apt-get install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev openjdk-8-jre", sep = "\n")
+ 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 python3 python3-dev python3-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 <- paste(result, "ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64", sep = "\n")
-
- }
+
+ result <- paste0(result, "\n")
- result <- paste0(result, "\n")
return(result)
}
@@ -227,13 +160,9 @@ createLibPrePost <- function(result) {
createRBase <- function(result) {
result <- paste(result, '############### Install R From RBase ##############', sep = "\n")
-
- if(input$containerType == "singularity") {
- result <- paste(result, "\tapt-get install -y r-base r-base-dev", sep = "\n")
- } else {
- result <- paste(result, "RUN apt-get install -y r-base r-base-dev", sep = "\n")
- }
-
+ result <- paste(result, "RUN apt-get install -y r-base r-base-dev", sep = "\n")
+ result <- paste0(result, "\n")
+ result <- paste0(result, "ENV R_VERSION=$(Rscript -e 'vers=paste(R.Version()[c(\"major\", \"minor\")], collapse = \".\"); cat(vers)')")
result <- paste0(result, "\n")
return(result)
}
@@ -243,25 +172,18 @@ createRSource <- function(result, Rversion) {
result <- paste(result, '############### Install R From Source ##############', sep = "\n")
- if(input$containerType == "singularity") {
- result <- paste(result, '\tcd $HOME', sep = "\n")
- result <- paste0(result, '\n\twget https://cran.rstudio.com/src/base/R-',strsplit(Rversion, "")[[1]][1],'/R-', Rversion, '.tar.gz')
- result <- paste0(result, '\n\ttar xvf R-', Rversion, '.tar.gz')
- result <- paste0(result, '\n\tcd R-', Rversion)
- result <- paste(result, "\t./configure --enable-R-static-lib --with-blas --with-lapack --enable-R-shlib=yes ", sep = "\n")
- result <- paste(result, "\tmake", sep = "\n")
- result <- paste(result, "\tmake install", sep = "\n")
- } else {
result <- paste(result, 'RUN cd $HOME \\', sep = "\n")
+ if( Rversion == "4.0.1")
+ result <- paste0(result, '\n\t&& wget https://cran.rstudio.com/src/base/R-4/R-', Rversion, '.tar.gz \\')
+ else
result <- paste0(result, '\n\t&& wget https://cran.rstudio.com/src/base/R-3/R-', Rversion, '.tar.gz \\')
+
result <- paste0(result, '\n\t&& tar xvf R-', Rversion, '.tar.gz \\')
result <- paste0(result, '\n\t&& cd R-', Rversion, ' \\')
result <- paste(result, "\t&& ./configure --enable-R-static-lib --with-blas --with-lapack --enable-R-shlib=yes \\", sep = "\n")
result <- paste(result, "\t&& make \\", sep = "\n")
result <- paste(result, "\t&& make install \\", sep = "\n")
- }
-
- result <- paste0(result, "\n")
+ result <- paste0(result, "\n")
return(result)
}
@@ -269,20 +191,11 @@ createRSource <- function(result, Rversion) {
createRCran <- function(result) {
result <- paste(result, '############### Install R From CRAN ##############', sep = "\n")
-
- if(input$containerType == "singularity") {
- result <- paste(result, "\tapt-get install -y software-properties-common", sep = "\n")
- result <- paste(result, "\tadd-apt-repository 'deb http://cloud.r-project.org/bin/linux/ubuntu xenial/'", sep = "\n")
- result <- paste(result, "\tapt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9", sep = "\n")
- result <- paste(result, "\tapt-get update", sep = "\n")
- result <- paste(result, "\tapt-get install -y r-base r-base-dev", sep = "\n")
- } else {
- result <- paste(result, "RUN apt-get install -y software-properties-common", sep = "\n")
- result <- paste(result, "RUN add-apt-repository 'deb http://cloud.r-project.org/bin/linux/ubuntu xenial/'", sep = "\n")
- result <- paste(result, "RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9", sep = "\n")
- result <- paste(result, "RUN apt-get update", sep = "\n")
- result <- paste(result, "RUN apt-get install -y r-base r-base-dev", sep = "\n")
- }
+ result <- paste(result, "RUN apt-get install -y software-properties-common", sep = "\n")
+ result <- paste(result, "RUN add-apt-repository 'deb http://cloud.r-project.org/bin/linux/ubuntu xenial/'", sep = "\n")
+ result <- paste(result, "RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9", sep = "\n")
+ result <- paste(result, "RUN apt-get update", sep = "\n")
+ result <- paste(result, "RUN apt-get install -y r-base r-base-dev", sep = "\n")
result <- paste0(result, "\n")
return(result)
@@ -291,23 +204,16 @@ createRCran <- function(result) {
#' Use for create CRAN content
createCRANPackage <- function(result) {
-
-
selectCRAN <- input$selectedCRAN
sizeCRAN <- length(selectCRAN)
-
- if(!is.null(sizeCRAN)) {
+ if(sizeCRAN > 0) {
if(sizeCRAN < length(allCRAN[,"Package"])) {
if(sizeCRAN >= 1) {
result <- paste(result, '############### Install CRAN Package ##############', sep = "\n")
- if(input$containerType == "singularity") {
- listRCRAN <- '\tR --slave -e "install.packages( c('
- } else {
- listRCRAN <- 'RUN R --slave -e "install.packages( c('
- }
+ listRCRAN <- 'RUN R --slave -e "install.packages( c('
for (pkg in 1:sizeCRAN){
if(pkg < sizeCRAN) {
@@ -338,13 +244,7 @@ createGithubPackage <- function(result) {
result <- paste(result, '############### Install Github Package ##############', sep = "\n")
-
- if(input$containerType == "singularity") {
- listRGITHUB <- '\tR --slave -e "install_github(c('
- } else {
- listRGITHUB <- 'RUN R --slave -e "install_github(c('
- }
-
+ listRGITHUB <- 'RUN R --slave -e "install_github(c('
for (pkg in 1:sizeGITHUB){
if(pkg < sizeGITHUB) {
@@ -369,9 +269,6 @@ createBioconductorPackage <- function(result) {
selectBIO <- input$selectedConductor
sizeBIO <- length(selectBIO)
-
-
-
if(!is.null(sizeBIO)) {
if(sizeBIO < length(allBIO[,"Package"])) {
if(sizeBIO >= 1) {
@@ -379,13 +276,9 @@ createBioconductorPackage <- function(result) {
result <- paste(result, '############### Install Bioconductor Package ##############', sep = "\n")
- if(input$containerType == "singularity") {
- result <- paste(result, '\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); biocLite(); "', sep = "\n")
- listRBIO <- '\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); biocLite('
- } else {
- result <- paste(result, 'RUN R --slave -e "source(\'https://bioconductor.org/biocLite.R\'); biocLite(); "', sep = "\n")
- listRBIO <- 'RUN R --slave -e "source(\'https://bioconductor.org/biocLite.R\'); biocLite('
- }
+ result <- paste(result, 'RUN R --slave -e "source(\'https://bioconductor.org/biocLite.R\'); biocLite(); "', sep = "\n")
+ listRBIO <- 'RUN R --slave -e "source(\'https://bioconductor.org/biocLite.R\'); biocLite('
+
for (pkg in 1:sizeBIO){
if(pkg < sizeBIO) {
@@ -407,19 +300,6 @@ createBioconductorPackage <- function(result) {
createPathWorkflow <- function(result) {
- if(input$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$selectedWorkflows
for (tool in selectBioTool){
@@ -431,8 +311,6 @@ createPathWorkflow <- function(result) {
}
- }
-
return(result)
}
@@ -440,19 +318,6 @@ createPathWorkflow <- function(result) {
createPathBiocontainer <- function(result) {
- if(input$containerType == "singularity") {
- selectBioTool <- input$selectedBiocontainer
- for (tool in selectBioTool){
-
- to <- getInstallToolEnvBioContainer(tool, input$containerType)
-
- if(is.character(to)) {
- result <- paste0(result, "\n\t", to)
- }
-
- }
-
- } else {
selectBioTool <- input$selectedBiocontainer
for (tool in selectBioTool){
@@ -464,91 +329,19 @@ createPathBiocontainer <- function(result) {
}
- }
-
return(result)
}
#' Use for create Workflows content
createWorkflows <- function(result, haveR, haveConda) {
- if(input$containerType == "singularity") {
- selectWorkflows <- input$selectedWorkflows
+ selectWorkflows <- input$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:$PATH\' > /etc/profile.d/conda.sh && \\",
- "\twget --quiet https://repo.continuum.io/miniconda/Miniconda2-4.0.5-Linux-x86_64.sh -O ./miniconda.sh && \\",
- "\t/bin/bash ./miniconda.sh -b -p /opt/conda && \\",
- "\trm ./miniconda.sh", sep = "\n")
-
- result <- paste0(result, "\n")
-
-
-
- result <- paste0(result, "\n")
-
- result <- paste(result, '\tif [ ! -d "/opt/biotools" ];then mkdir /opt/biotools; fi', sep = "\n")
- result <- paste(result, '\tif [ ! -d "/opt/biotools/bin" ];then mkdir /opt/biotools/bin; fi', sep = "\n")
- result <- paste(result, "\tchmod 777 -R /opt/biotools/", sep = "\n")
- result <- paste(result, "\texport PATH=/opt/biotools/bin:$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 ##############\n', sep = "\n")
-
-
- for(i in getInstallToolPackageWorkflow(tool, input$containerType)) {
- result <- paste0(result, i, "\n")
- }
-
- }
- } else {
- selectWorkflows <- input$selectedWorkflows
-
- 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:$PATH\' > /etc/profile.d/conda.sh && \\",
- "\twget --quiet https://repo.continuum.io/miniconda/Miniconda2-4.0.5-Linux-x86_64.sh -O ./miniconda.sh && \\",
- "\t/bin/bash ./miniconda.sh -b -p /opt/conda && \\",
- "\trm ./miniconda.sh", sep = "\n")
-
- result <- paste0(result, "\n")
-
-
+
result <- paste0(result, "\n")
@@ -557,17 +350,15 @@ createWorkflows <- function(result, haveR, haveConda) {
result <- paste(result, "RUN chmod 777 -R /opt/biotools/", sep = "\n")
result <- paste(result, "ENV PATH=/opt/biotools/bin:${PATH}", sep = "\n")
- result <- paste(result, "RUN chmod 777 -R /opt/conda/", sep = "\n")
- result <- paste(result, "ENV PATH=/opt/conda/bin:${PATH}", sep = "\n")
+
+
+ result <- paste0(result, "\n")
if(!haveR) {
result <- paste(result, "RUN conda config --add channels r", sep = "\n")
}
- result <- paste(result, "RUN conda config --add channels bioconda", sep = "\n")
- result <- paste(result, "RUN conda upgrade conda", sep = "\n")
-
- result <- paste0(result, "\n")
+
}
@@ -585,7 +376,7 @@ createWorkflows <- function(result, haveR, haveConda) {
}
}
- }
+
result <- paste0(result, "\n")
return(result)
@@ -595,68 +386,11 @@ createWorkflows <- function(result, haveR, haveConda) {
#' Use for create Biocontainer content
createBiocontainer <- function(result, haveR) {
- if(input$containerType == "singularity") {
- selectBioTool <- input$selectedBiocontainer
-
- result <- paste0(result, "\n")
-
- result <- paste(result, "\tapt-get install -y autotools-dev automake cmake curl grep sed dpkg fuse git zip openjdk-8-jre build-essential pkg-config python python-dev python-pip bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev libncurses5-dev libncursesw5-dev", sep = "\n")
- result <- paste(result, "\tapt-get update", sep = "\n")
-
- result <- paste0(result, "\n")
-
- result <- paste(result, "\techo \'export PATH=/opt/conda/bin:$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 <- 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")
-
- for (tool in selectBioTool){
-
- result <- paste(result, '############### Install BioContainer tools ##############\n', sep = "\n")
-
-
- result <- paste(result, getInstallToolPackageBioContainer(tool, input$containerType), sep="\n\n")
- }
- } else {
+
selectBioTool <- input$selectedBiocontainer
result <- paste0(result, "\n")
- 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:$PATH\' > /etc/profile.d/conda.sh && \\",
- "\twget --quiet https://repo.continuum.io/miniconda/Miniconda2-4.0.5-Linux-x86_64.sh -O ./miniconda.sh && \\",
- "\t/bin/bash ./miniconda.sh -b -p /opt/conda && \\",
- "\trm ./miniconda.sh", sep = "\n")
-
- result <- paste0(result, "\n")
-
-
result <- paste0(result, "\n")
result <- paste(result, "RUN mkdir /opt/biotools", sep = "\n")
@@ -664,28 +398,18 @@ createBiocontainer <- function(result, haveR) {
result <- paste(result, "RUN chmod 777 -R /opt/biotools/", sep = "\n")
result <- paste(result, "ENV PATH=/opt/biotools/bin:${PATH}", sep = "\n")
- result <- paste(result, "RUN chmod 777 -R /opt/conda/", sep = "\n")
- result <- paste(result, "ENV PATH=/opt/conda/bin:${PATH}", sep = "\n")
if(!haveR) {
result <- paste(result, "RUN conda config --add channels r", sep = "\n")
}
- result <- paste(result, "RUN conda config --add channels bioconda", sep = "\n")
- result <- paste(result, "RUN conda upgrade conda", sep = "\n")
-
- result <- paste0(result, "\n")
+
+ result <- paste(result, '############### Install BioContainer tools ##############\n', sep = "\n")
for (tool in selectBioTool){
-
- result <- paste(result, '############### Install BioContainer tools ##############\n', sep = "\n")
-
-
- result <- paste0(result, "RUN ", getInstallToolPackageBioContainer(tool, input$containerType))
+ result <- paste0(result, "RUN ", getInstallToolPackageBioContainer(tool, input$containerType),"\n")
}
-
- }
-
+
result <- paste0(result, "\n")
return(result)
}
@@ -700,7 +424,17 @@ createContentFile <- function() {
result <- createLabel(result)
result <- createLibPrePost(result)
- if(input$rtemplate != "none" && input$fromTemplate != "r-base") {
+ selectCRAN <- input$selectedCRAN
+ sizeCRAN <- length(selectCRAN)
+
+ selectBIO <- input$selectedConductor
+ sizeBIO <- length(selectBIO)
+
+ selectGithub <- input$rgithubpackagelist
+ sizeGITHUB <- length(selectGithub)
+
+ if (!is.null(sizeCRAN) ) print(sizeCRAN)
+ if(input$rtemplate != "none" | sizeCRAN > 0 | sizeBIO > 0 | sizeGITHUB > 0) {
haveR = TRUE
@@ -716,7 +450,7 @@ createContentFile <- function() {
Rversion = "4.0.1"
}
result <- createRSource(result, Rversion)
- } else if(input$rtemplate == "base") {
+ } else if(input$rtemplate == "base" | input$rtemplate == "none") {
result <- createRBase(result)
} else if(input$rtemplate == "cran") {
result <- createRCran(result)
@@ -724,9 +458,9 @@ createContentFile <- function() {
}
- result <- createCRANPackage(result)
- result <- createBioconductorPackage(result)
- result <- createGithubPackage(result)
+ result <- createCRANPackage(result)
+ result <- createBioconductorPackage(result)
+ result <- createGithubPackage(result)
haveBiocontainer <- FALSE
if(!is.null(input$selectedBiocontainer)) {
@@ -751,6 +485,25 @@ observeEvent(input$createContainer, {
result <- createContentFile()
+ if(input$containerType == "singularity") {
+ # will convert result using spython https://singularityhub.github.io/
+ #save result in a tmp file
+ dockerfile = tempfile(pattern = "Dockerfile")
+ tmpSingularityFile = tempfile(pattern = "Singularity")
+ write.table(result, dockerfile, row.names=F, col.names=F, quote=F)
+ cmd = paste0("sed -i 's/R_VERSION=.*/R_VERSION=getRversion/' ",dockerfile)
+ system(cmd)
+ cmd = paste0("spython recipe ", dockerfile, " > ", tmpSingularityFile)
+ system(cmd)
+ # read tmpSingularityFile in result var
+ cmd = paste0("sed -i 's/getRversion/$(Rscript -e \"vers=paste(R.Version()[c(\"major\",\"minor\")],collapse =\".\");cat(vers)\")/' ", tmpSingularityFile)
+ system(cmd)
+
+ result <- paste(readLines(tmpSingularityFile, n=-1),"\n", collapse = '')
+ unlink(dockerfile)
+ unlink(tmpSingularityFile)
+
+ }
updateTextAreaInput(session, "previewContainer",
label = "",
value = result)
@@ -778,11 +531,8 @@ observeEvent(input$createContainer, {
output$downloadContainerFile <- downloadHandler(
filename = function() {
name <- ""
- if(input$containerType == "singularity") {
- name <- paste("Singularity",input$imageName, sep = ".")
- } else {
- name <- paste("Dockerfile",input$imageName, sep = ".")
- }
+ name <- paste("Dockerfile",input$imageName, sep = ".")
+
},
content = function(file) {
result <- input$previewContainer
--
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