pages_def_home.R 7.79 KB
Newer Older
jlopez's avatar
Proto  
jlopez committed
1
tabHome = fluidPage(align="left",
jlopez's avatar
jlopez committed
2
3
4
5
6
7
8
9
10
                    
                    column(width = 12,
                           box(
                             title = "Help",
                             width = NULL,
                             collapsible = TRUE,
                             status="primary",
                             solidHeader = TRUE,
                             tags$b("Bioinformatics tools: "),
khalid's avatar
khalid committed
11
                             p("Select each tool by clicking on the corresponding field in the table. "),
jlopez's avatar
jlopez committed
12
                             br(),
khalid's avatar
khalid committed
13
14
                             tags$b("CRAN R Packages: "),
                             p("Search your package in the filed 'Package' and click on the name of your package to select it."),
jlopez's avatar
jlopez committed
15
                             br(),
khalid's avatar
khalid committed
16
17
                             tags$b("Bioconductor R Packages: "),
                             p("Search your package in the filed 'Package' and click on the name of your package to select it."),
jlopez's avatar
jlopez committed
18
19
                             br(),
                             tags$b("Github R Packages: "),
khalid's avatar
khalid committed
20
21
                             p("Add your tools by clicking on the corresponding field in the table. They appear in the field so below."),
                             br(),
jlopez's avatar
jlopez committed
22
                             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."),
khalid's avatar
khalid committed
23
24
25
26
27
                             p("# To build the image from the recipes file named ubuntu6.10_stacks2.0.simg :"),
                             p("sudo singularity build ubuntu6.10_stacks2.0.simg ubuntu6.10_stacks2.0.recipes"),
                             p("# to run a program inside the image container :"),
                             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'")
jlopez's avatar
jlopez committed
28
                           )),
jlopez's avatar
Proto  
jlopez committed
29
30
31
32
33
34
35
36
37
38
39
  
                    column(width = 2,
                           box(
                               title = "Params",
                               width = NULL,
                               collapsible = TRUE,
                               solidHeader = TRUE,
                               status="primary",
                               
                               textInput("imageName", "Image Name", ""),
                               br(),
jlopez's avatar
Fix    
jlopez committed
40
                               selectizeInput('fromTemplate', 'From:', choices = c(`ubuntu:16.04` = 'ubuntu:16.04', `r-base` = 'r-base'), selected = "r-base", multiple = FALSE),
jlopez's avatar
jlopez committed
41
                               br(),
jlopez's avatar
jlopez committed
42
                               radioButtons("containerType", "Container type:", choices = list("Singularity" = "singularity", "Docker" = "docker"), selected = "singularity"),
jlopez's avatar
Proto  
jlopez committed
43
                               br(),
jlopez's avatar
Fix bug    
jlopez committed
44
                               #selectizeInput('rcranpackagelist', 'R CRAN:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
jlopez's avatar
Fix    
jlopez committed
45
                               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),
jlopez's avatar
jlopez committed
46
47
48
49
                               #selectizeInput('biocontainers', 'BioContainers tools :', choices = getBioconductorPackage(), multiple = TRUE),
                               
                               
                               
jlopez's avatar
Proto  
jlopez committed
50
51
                               textAreaInput("customDataContainer", "Add custom line to container file:"),
                               br(), br(),
jlopez's avatar
jlopez committed
52
                              
jlopez's avatar
jlopez committed
53
                               actionButton("createContainer", label = "Generate", icon("paper-plane"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
jlopez's avatar
Proto  
jlopez committed
54
55
56
57
58
                               downloadButton('downloadContainerFile', label = "Dowload",  style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
                               
                           )),
                    column(width = 10,
                           box(
jlopez's avatar
jlopez committed
59
                             id = "boxPackage",
jlopez's avatar
jlopez committed
60
                             title = "Packages and tools",
jlopez's avatar
Proto  
jlopez committed
61
62
63
64
65
                             width = NULL,
                             collapsible = TRUE,
                             solidHeader = TRUE,
                             status="primary",
                             tabsetPanel( id='rpackages',
jlopez's avatar
jlopez committed
66
67
68
69
                                          tabPanel('Bioinformatics tools',
                                                   div(id = "formContainer",
                                                       br(),
                                                       selectizeInput('selectedBiocontainer', 'Biocontainer tools selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000))),
jlopez's avatar
jlopez committed
70
                                                   
jlopez's avatar
jlopez committed
71
72
                                                   DT::dataTableOutput('dtbiocontainer')
                                          ),
jlopez's avatar
jlopez committed
73
74
75
76
77
78
79
                                          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")
                                                  )
jlopez's avatar
Proto  
jlopez committed
80
                                          ),
jlopez's avatar
jlopez committed
81
                                          tabPanel('Bioconductor Packages',   
jlopez's avatar
jlopez committed
82
83
84
                                            div(id = "formBioconductor",
                                            #  br(),
                                            #selectizeInput('selectedBioconductor', 'R Bioconductor selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
jlopez's avatar
jlopez committed
85
                                            selectizeInput('selectedConductor', 'Bioconductor package selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
jlopez's avatar
jlopez committed
86
                                            
jlopez's avatar
jlopez committed
87
                                            DT::dataTableOutput('dtrbioconductorpackage'))),
jlopez's avatar
jlopez committed
88
                                          tabPanel('Github R Packages',
jlopez's avatar
jlopez committed
89
90
                                            textInput("inputGithub", "Package name:", ""),
                                            actionButton("findGithub", label = "Find", icon("paper-plane"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),
jlopez's avatar
jlopez committed
91
                                            div(id = "formGithub",
jlopez's avatar
jlopez committed
92
                                            br(), br(),
jlopez's avatar
jlopez committed
93
                                            selectizeInput('rgithubpackagelist', 'R Github selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
jlopez's avatar
jlopez committed
94
                                            
jlopez's avatar
jlopez committed
95
                                            br(), br(),
jlopez's avatar
jlopez committed
96
97
                                            DT::dataTableOutput('dtrgithubpackage')))
                                          
jlopez's avatar
Proto  
jlopez committed
98
99
100
101
102
103
104
105
106
107
108
                             )
                          )
                    ),
                    column(width = 12,
                           box(
                             title = "Preview File:",
                             width = NULL,
                             collapsible = TRUE,
                             solidHeader = TRUE,
                             status="primary",
                             style='height:1000px; overflow-y: scroll',
jlopez's avatar
jlopez committed
109
                             textAreaInput("previewContainer", label = "", height = "1000px")
jlopez's avatar
Proto  
jlopez committed
110
111
112
113
                           )
                    )
                    
)