pages_def_home.R 8.45 KB
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tabHome = fluidPage(align="left",
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                    column(width = 12,
                           box(
                             title = "Help",
                             width = NULL,
                             collapsible = TRUE,
                             status="primary",
                             solidHeader = TRUE,
                             tags$b("Bioinformatics tools: "),
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                             p("Select each tool by clicking on the corresponding field in the table. They appear in the field below."),
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                             tags$b("CRAN R Packages: "),
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                             p("Select each tool by clicking on the corresponding field in the table. They appear in the field below."),
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                             tags$b("Bioconductor R Packages: "),
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                             p("Select each tool by clicking on the corresponding field in the table. They appear in the field below."),
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                             tags$b("Github R Packages: "),
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                             p("Select each tool by clicking on the corresponding field in the table. They appear in the field below."),
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                             p("Use 'Generate' button to generate your recipe in the preview area then copy/paste the text or use dowload button to get your file."),
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                             tags$b("For Singularity containers: To build the image from the recipes file named ubuntu6.10_stacks2.0.simg :"),
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                             p("sudo singularity build ubuntu6.10_stacks2.0.simg ubuntu6.10_stacks2.0.recipes"),
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                             tags$b("To run a program inside the image container :"),
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                             p(" singularity exec ubuntu6.10_stacks2.0.simg python --version "),
                             p("singularity exec ubuntu6.10_stacks2.0.simg python -c 'import pysam; print 2*2'")
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                           )),
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                    column(width = 2,
                           box(
                               title = "Params",
                               width = NULL,
                               collapsible = TRUE,
                               solidHeader = TRUE,
                               status="primary",
                               
                               textInput("imageName", "Image Name", ""),
                               br(),
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                               #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'), selected = "ubuntu:16.04", multiple = FALSE),
                               
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                               br(),
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                               radioButtons("containerType", "Container type:", choices = list("Singularity" = "singularity", "Docker" = "docker"), selected = "singularity"),
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                               br(),
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                               #selectizeInput('rcranpackagelist', 'R CRAN:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
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                               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 r-base` = 'base', `R from CRAN depo` = 'cran'), selected = "none", multiple = FALSE),
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                               #selectizeInput('biocontainers', 'BioContainers tools :', choices = getBioconductorPackage(), multiple = TRUE),
                               
                               
                               
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                               textAreaInput("customDataContainer", "Add custom line to container file:"),
                               br(), br(),
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                               actionButton("createContainer", label = "Generate", icon("paper-plane"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
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                               downloadButton('downloadContainerFile', label = "Dowload",  style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
                               
                           )),
                    column(width = 10,
                           box(
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                             id = "boxPackage",
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                             title = "Packages and tools",
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                             width = NULL,
                             collapsible = TRUE,
                             solidHeader = TRUE,
                             status="primary",
                             tabsetPanel( id='rpackages',
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                                          tabPanel('Bioinformatics tools',
                                                   div(id = "formContainer",
                                                       br(),
                                                       selectizeInput('selectedBiocontainer', 'Biocontainer tools selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000))),
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                                                   DT::dataTableOutput('dtbiocontainer')
                                          ),
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                                          tabPanel('CRAN Packages', 
                                                   div(id = "formCRAN",
                                                    selectizeInput('selectedCRAN', 'CRAN package selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000))
                                                   ,
                                          
                                                    withSpinner(DT::dataTableOutput('dtrcranpackage'), type = 4, proxy.height = "150px")
                                                  )
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                                          ),
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                                          tabPanel('Bioconductor Packages',   
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                                            div(id = "formBioconductor",
                                            #  br(),
                                            #selectizeInput('selectedBioconductor', 'R Bioconductor selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
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                                            selectizeInput('selectedConductor', 'Bioconductor package selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
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                                            DT::dataTableOutput('dtrbioconductorpackage'))),
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                                          tabPanel('Github R Packages',
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                                            textInput("inputGithub", "Package name:", ""),
                                            actionButton("findGithub", label = "Find", icon("paper-plane"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
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                                            div(id = "formGithub",
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                                            br(), br(),
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                                            selectizeInput('rgithubpackagelist', 'R Github selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
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                                            br(), br(),
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                                            DT::dataTableOutput('dtrgithubpackage'))),
                                         
                                          tabPanel('Workflows',
                                            div(id = "formWorkflows",
                                              br(),
                                              selectizeInput('selectedWorkflows', 'Workflows selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000))),
                                                              
                                              DT::dataTableOutput('dtWorkflows'))
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                             )
                          )
                    ),
                    column(width = 12,
                           box(
                             title = "Preview File:",
                             width = NULL,
                             collapsible = TRUE,
                             solidHeader = TRUE,
                             status="primary",
                             style='height:1000px; overflow-y: scroll',
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                             textAreaInput("previewContainer", label = "", height = "1000px")
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                           )
                    )
                    
)