Merge pull request #72 from duocang/modulization

deploy PMET-shiny-app with docker

01_deploy_via_Docker.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+source scripts/colored_print.sh
+source scripts/check_and_set_email_credentials.sh
+source scripts/check_CPU_number.sh
+set -e
+
+#################### 1 email
+print_green "1. Configurations of email to send results"
+check_and_set_email_credentials
+
+#################### 2. CPU
+print_green "2. Configuration of CPU number"
+check_cpu_number
+
+#################### 3. Docker build
+print_green "3. Docker building"
+chmod  777 logs result
+docker-compose up -d

R/R_packages_installation.log

@@ -0,0 +1,46 @@
+[1] TRUE
+[1] TRUE
+[1] TRUE
+character(0)
+
+The installed packages are as follows:
+ [1] "av"                       "bslib"                   
+ [3] "daattali/shinycssloaders" "daattali/shinydisconnect"
+ [5] "data.table"               "datawookie/emayili"      
+ [7] "devtools"                 "dplyr"                   
+ [9] "dreamRs/shinybusy"        "dreamRs/shinyWidgets"    
+[11] "DT"                       "emayili"                 
+[13] "enrichplot"               "future"                  
+[15] "gapminder"                "ggasym"                  
+[17] "ggplot2"                  "ggpubr"                  
+[19] "glue"                     "Hmisc"                   
+[21] "httpuv"                   "jhrcook/ggasym"          
+[23] "kableExtra"               "magick"                  
+[25] "merlinoa/shinyFeedback"   "msigdbr"                 
+[27] "openxlsx"                 "pak"                     
+[29] "pdftools"                 "plotly"                  
+[31] "promises"                 "pryr"                    
+[33] "qpdf"                     "r-lib/ragg"              
+[35] "r-lib/rlang"              "r-lib/systemfonts"       
+[37] "r-lib/textshaping"        "r-lib/usethis"           
+[39] "r-rust/gifski"            "ragg"                    
+[41] "RcppRoll"                 "reshape2"                
+[43] "RinteRface/fullPage"      "rintrojs"                
+[45] "rJava"                    "rlang"                   
+[47] "rstudio/httpuv"           "rsvg"                    
+[49] "rtracklayer"              "scales"                  
+[51] "seqinr"                   "shiny"                   
+[53] "shinyBS"                  "shinybusy"               
+[55] "shinycssloaders"          "shinydashboard"          
+[57] "shinydisconnect"          "shinyFeedback"           
+[59] "shinyjs"                  "shinythemes"             
+[61] "shinyvalidate"            "shinyWidgets"            
+[63] "stringr"                  "svglite"                 
+[65] "systemfonts"              "tesseract"               
+[67] "textshaping"              "tibble"                  
+[69] "tictoc"                   "tidyverse"               
+[71] "usethis"                  "xfun"                    
+[73] "xlsxjars"                 "zip"                     
+
+The following packages could not be installed:
+[1] "pander"

R/app.R

@@ -1,3 +1,6 @@
+Sys.setenv(R_LIBS_USER = "/usr/local/lib/R/library")
+.libPaths(new = "/usr/local/lib/R/library")
+
 source("R/global.R")
 
 ui <- fluidPage(

R/global.R

@@ -1,52 +1,102 @@
+Sys.setenv(R_LIBS_USER = "/usr/local/lib/R/library")
+.libPaths(new = "/usr/local/lib/R/library")
+
+options(shiny.maxRequestSize = 30000 * 1024^2)
+
 suppressMessages({
-  # Used packages
-  pacotes <- c(
-    "bslib",              # customizing the appearance of Shiny applications using Bootstrap.
-    "data.table",         # fast data manipulation and analysis.
-    "DT",                 # creating interactive and customizable data tables in R.
-    "dplyr",              # data manipulation and transformation using a consistent grammar.
-    "fullPage",           # creating full-page scrolling websites.
-    "future",
-    "ggasym",             # creating asymmetric visualizations with ggplot2.
-    "ggpubr",             # enhancing ggplot2 visualizations with publication-ready themes and annotations.
-    "glue",               # interpolating strings and expressions in R.
-    "jsonify",
-    "kableExtra",         # creating complex tables in R Markdown documents.
-    "openxlsx",           # reading, writing, and manipulating Microsoft Excel files.
-    "promises",           # creating and managing asynchronous programming in R.
-    "purrr",              # functional programming and iterating over data structures.
-    "reshape2",           # transforming and restructuring data in R.
-    "rintrojs",           # creating interactive and guided tours in Shiny applications.
-    "rjson",              # converts R object into JSON objects and vice-versa.
-    "rtracklayer",        # read gff3
-    "scales",             # controlling the scaling of data in R graphics.
-    "seqinr",             # extract fasta's name
-    "shiny",              # building interactive web applications in R.
-    "shinyBS",            # adding additional Bootstrap functionality to Shiny applications.
-    "shinybusy",          # Automated (or not) busy indicator for Shiny apps & other progress / notifications tools
-    "shinydashboard",     # creating dashboards with a tabbed layout in Shiny.
-    "shinydisconnect",    # handling disconnections and reconnections in Shiny applications.
-    "shinyFeedback",      # providing user feedback and notifications in Shiny applications.
-    "shinycssloaders",    # adding CSS loaders to Shiny applications.
-    "shinyjs",            # easily incorporating JavaScript functions and events in Shiny applications.
-    "shinythemes",        # customizing the appearance of Shiny applications with predefined themes.
-    "shinyvalidate",      # client-side form validation in Shiny applications.
-    "shinyWidgets",       # creating custom UI controls and widgets in Shiny.
-    "snow",               # parallel computing using a simple network of workstations.
-    "tibble",             # creating and manipulating data frames with enhanced features compared to traditional data frames.
-    "tidyverse",          # data manipulation, visualization, and analysis.
-    "tictoc",             # measuring the time taken by R code execution.
-    "shinyvalidate",      # shinyvalidate adds input validation capabilities to Shiny.
-    "zip"                 # reading, writing, and manipulating ZIP archives in R.
-)
-
-  # verify required packages installed or not. If some package
-  # is missing, it will be installed automatically
-  package.check <- lapply(pacotes, FUN = function(x) {
-    if (!require(x, character.only = TRUE)) {
-      install.packages(x, dependencies = TRUE)
-    }
-  })
+#   # Used packages
+#   pacotes <- c(
+#     "emayili",
+#     "bslib",              # customizing the appearance of Shiny applications using Bootstrap.
+#     "data.table",         # fast data manipulation and analysis.
+#     "DT",                 # creating interactive and customizable data tables in R.
+#     "dplyr",              # data manipulation and transformation using a consistent grammar.
+#     "fullPage",           # creating full-page scrolling websites.
+#     "future",
+#     "ggasym",             # creating asymmetric visualizations with ggplot2.
+#     "ggpubr",             # enhancing ggplot2 visualizations with publication-ready themes and annotations.
+#     "glue",               # interpolating strings and expressions in R.
+#     "kableExtra",         # creating complex tables in R Markdown documents.
+#     "openxlsx",           # reading, writing, and manipulating Microsoft Excel files.
+#     "promises",           # creating and managing asynchronous programming in R.
+#     "purrr",              # functional programming and iterating over data structures.
+#     "reshape2",           # transforming and restructuring data in R.
+#     "rintrojs",           # creating interactive and guided tours in Shiny applications.
+#     "rjson",              # converts R object into JSON objects and vice-versa.
+#     "rtracklayer",        # read gff3
+#     "scales",             # controlling the scaling of data in R graphics.
+#     "seqinr",             # extract fasta's name
+#     "shiny",              # building interactive web applications in R.
+#     "shinyBS",            # adding additional Bootstrap functionality to Shiny applications.
+#     "shinybusy",          # Automated (or not) busy indicator for Shiny apps & other progress / notifications tools
+#     "shinydisconnect",    # handling disconnections and reconnections in Shiny applications.
+#     "shinyFeedback",      # providing user feedback and notifications in Shiny applications.
+#     "shinycssloaders",    # adding CSS loaders to Shiny applications.
+#     "shinyjs",            # easily incorporating JavaScript functions and events in Shiny applications.
+#     "shinythemes",        # customizing the appearance of Shiny applications with predefined themes.
+#     "shinyvalidate",      # client-side form validation in Shiny applications.
+#     "shinyWidgets",       # creating custom UI controls and widgets in Shiny.
+#     "snow",               # parallel computing using a simple network of workstations.
+#     "tibble",             # creating and manipulating data frames with enhanced features compared to traditional data frames.
+#     "tidyverse",          # data manipulation, visualization, and analysis.
+#     "tictoc",             # measuring the time taken by R code execution.
+#     "shinyvalidate",      # shinyvalidate adds input validation capabilities to Shiny.
+#     "zip"                 # reading, writing, and manipulating ZIP archives in R.
+# )
+
+# #   # verify required packages installed or not. If some package
+# #   # is missing, it will be installed automatically
+# #   package.check <- lapply(pacotes, FUN = function(x) {
+# #     if (!require(x, character.only = TRUE)) {
+# #       print(x)
+# #       install.packages(x, dependencies = TRUE)
+# #     }
+# #   })
+
+#   # 循环引入包
+#   lapply(pacotes, function(pkg) {
+#     requireNamespace(pkg, quietly = TRUE)
+#     library(pkg, character.only = TRUE)
+#   })
+
+  # 显式地调用packages是因为renv的package管理需要识别library
+  library(jsonlite)
+  library(emayili)
+  library(bslib)
+  library(data.table)
+  library(DT)
+  library(dplyr)
+  library(fullPage)
+  library(future)
+  library(ggasym)
+  library(ggpubr)
+  library(glue)
+  library(kableExtra)
+  library(openxlsx)
+  library(promises)
+  library(purrr)
+  library(reshape2)
+  library(rintrojs)
+  library(rjson)
+  library(rtracklayer)
+  library(scales)
+  library(seqinr)
+  library(shiny)
+  library(shinyBS)
+  library(shinybusy)
+  library(shinydisconnect)
+  library(shinyFeedback)
+  library(shinycssloaders)
+  library(shinyjs)
+  library(shinythemes)
+  library(shinyvalidate)
+  library(shinyWidgets)
+  library(snow)
+  library(tibble)
+  library(tidyverse)
+  library(tictoc)
+  library(shinyvalidate)
+  library(zip)
 
   source("R/utils/utils.R")
   source("R/utils/shiny_busy_indicator.R")
@@ -66,23 +116,21 @@ suppressMessages({
   source("R/utils/motif_pair_gene_diagonal.R")
 })
 
-options(shiny.maxRequestSize = 30000 * 1024^2)
-plan(multisession)
-
-
-cpu_configuration <- readLines("data/cpu_configuration.txt")
-NCPU <- cpu_configuration[1]
+NCPU <- readLines("data/cpu_configuration.txt")[1]
 
-# to detect the pre-computed motif-DB data
-# when new daata comes, there is no need to change code.
+# auto detect the pre-computed motif-DB data: when new species or motif database comes, no need to change code.
 species <- list.dirs("./data/indexing", recursive=F) %>%
   sapply(function(i) {
     str <- stringr::str_split_1(i, "/")[4] # %>% tolower() #%>% gsub("(^|\\s)([a-z])", "\\1\\U\\2", ., perl = TRUE) # capitablize first letter
     return(str)
   })
 # > species
-# ./data/indexing/arabidopsis_thaliana         ./data/indexing/mais
-#               "arabidopsis_thaliana"                       "mais"
+# ./data/indexing/Arabidopsis_thaliana
+#                 "Arabidopsis_thaliana"
+# ./data/indexing/Brachypodium_distachyon
+#               "Brachypodium_distachyon"
+#         ./data/indexing/Brassica_napus
+#                       "Brassica_napus"
 
 MOTIF_DB <- lapply(species, function(speci) {
 
@@ -93,10 +141,24 @@ MOTIF_DB <- lapply(species, function(speci) {
   for (i in seq(length(motif_dbs))) {
     result[[ list_names[i] ]] <- file.path("data/indexing", speci , motif_dbs[i])
   }
-
   return(result)
 }) %>% setNames(unname(species))
+# > MOTIF_DB
+# $Arabidopsis_thaliana
+# $Arabidopsis_thaliana$`CIS-BP2`
+# [1] "data/indexing/Arabidopsis_thaliana/CIS-BP2"
+
+# $Arabidopsis_thaliana$`Franco-Zorrilla et al 2014`
+# [1] "data/indexing/Arabidopsis_thaliana/Franco-Zorrilla_et_al_2014"
+
+# $Arabidopsis_thaliana$`Jaspar plants non redundant 2022`
+# [1] "data/indexing/Arabidopsis_thaliana/Jaspar_plants_non_redundant_2022"
 
+# $Arabidopsis_thaliana$`Plant Cistrome DB`
+# [1] "data/indexing/Arabidopsis_thaliana/Plant_Cistrome_DB"
+
+# $Arabidopsis_thaliana$PlantTFDB
+# [1] "data/indexing/Arabidopsis_thaliana/PlantTFDB"
 
 SPECIES_LIST <- list()
 
@@ -105,5 +167,27 @@ for (speci in species) {
   SPECIES_LIST[[temp]] <- speci
 }
 SPECIES_LIST <- list(species = SPECIES_LIST) # to show nothing first of fileInput box
+# > SPECIES_LIST
+# $species
+# $species$`Arabidopsis thaliana`
+# [1] "Arabidopsis_thaliana"
+
+# $species$`Brachypodium distachyon`
+# [1] "Brachypodium_distachyon"
+
+# $species$`Brassica napus`
+# [1] "Brassica_napus"
+
+# $species$`Glycine max`
+# [1] "Glycine_max"
+
+MOTF_DB_META <- rjson::fromJSON(file = "data/motif_db_meta.json")
+# > MOTF_DB_META
+# $Arabidopsis_thaliana
+# $Arabidopsis_thaliana$genome_name
+# [1] "Arabidopsis_thaliana.TAIR10.dna.toplevel.fa"
+
+# $Arabidopsis_thaliana$annotation_name
+# [1] "Arabidopsis_thaliana.TAIR10.56.gff3"
 
-MOTF_DB_META <- fromJSON(file = "data/motif_db_meta.json")
+# $Arabidopsis_thaliana$genome_link

R/server/tab_visualize.R

@@ -381,3 +381,4 @@ observeEvent(pmet.result.processed(), {
   })
   server_data("pmet_talble_tab", result)
 })
+

R/ui/tab_test.R

@@ -1,3 +1,30 @@
+# tabPanel(
+#   title = "Test",
+#   value = "Test_tabpanel",
+#   tags$head(
+#     tags$link(rel = "stylesheet", href = "https://cdnjs.cloudflare.com/ajax/libs/fullPage.js/3.1.2/fullpage.min.css"),
+#     tags$script(src = "https://cdnjs.cloudflare.com/ajax/libs/fullPage.js/3.1.2/fullpage.min.js")
+#   ),
+#   tags$script("
+#     $(document).ready(function() {
+#       new fullpage('#my-fullpage', {
+#         // fullPage.js options
+#       });
+#     });
+#   "),
+#   div(id = "my-fullpage",
+#     div(class = "section",
+#       actionButton("a", "a"),
+#       h1("Section 1")
+#     ),
+#     div(class = "section",
+#       h1("Section 2")
+#     ),
+#     div(class = "section",
+#       h1("Section 3")
+#     )
+#   )
+# )
 tabPanel(
   class = "tabPanel_shiny",
   "My Tab",