bring some readme to the code

DESCRIPTION

@@ -4,8 +4,9 @@ Title: Templates and functions to guide downstream analysis and data interpretat
 Version: 0.1.0
 Authors@R: person("Pantano", "Lorena", , "lorena.pantano@gmail.com",
             role = c("aut", "cre"))
-Description: Collaborative code repository from the Harvard Chan Bioinformatics Core.
+Description: Collaborative code repository at the Harvard Chan Bioinformatics Core.
 License: MIT + file LICENSE
 LazyData: true
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1

NAMESPACE

@@ -1 +1,4 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(bcbio_set_project)
+export(bcbio_start_project)

R/hello.R

@@ -13,7 +13,68 @@
 #   Check Package:             'Cmd + Shift + E'
 #   Test Package:              'Cmd + Shift + T'
 
+#' @export
+bcbio_set_project <- function() {
+  hbc_code <- readline("What is the hbc code:\n")
+  project <- readline("What is the project name:\n")
+  dropbox <- readline("What is the dropbox name:\n")
+  github_org <- readline("What is the github organization:\n")
+  project_full <- paste0(project, "_", hbc_code)
+  github <- c(github_org,project_full)
+  opts <- list(code=hbc_code, project=project_full,
+               dropbox=file.path(dropbox,project_full),
+               github=github)
+  print(opts)
+  return(opts)
+}
+
+#' @export
+bcbio_start_project <- function(options) {
+
+}
+
 hello <- function() {
   print("Hello, world!")
 
 }
+
+# This function showcases how one might write a function to be used as an
+# RStudio project template. This function will be called when the user invokes
+# the New Project wizard using the project template defined in the template file
+# at:
+#
+#   inst/rstudio/templates/project/hello_world.dcf
+#
+# The function itself just echos its inputs and outputs to a file called INDEX,
+# which is then opened by RStudio when the new project is opened.
+rnaseq <- function(path, ...) {
+
+  # ensure path exists
+  dir.create(path, recursive = TRUE, showWarnings = FALSE)
+
+  # generate header
+  header <- c(
+    "# This file was generated by a call to 'ptexamples::hello_world()'.",
+    "# The following inputs were received:",
+    ""
+  )
+
+  # collect inputs
+  dots <- list(...)
+  text <- lapply(seq_along(dots), function(i) {
+    key <- names(dots)[[i]]
+    val <- dots[[i]]
+    paste0(key, ": ", val)
+  })
+
+  # collect into single text string
+  contents <- paste(
+    paste(header, collapse = "\n"),
+    paste(text, collapse = "\n"),
+    sep = "\n"
+  )
+
+  # write to index file
+  writeLines(contents, con = file.path(path, "README.md"))
+
+}

inst/rmarkdown/templates/project/rnaseq.dcf

@@ -0,0 +1,28 @@
+Binding: rnaseq
+Title: RNAseq Analysis
+OpenFiles: README.md
+
+Parameter: check
+Widget: CheckboxInput
+Label: Checkbox Input
+Default: On
+Position: left
+
+Parameter: select
+Widget: SelectInput
+Label: Select Input
+Fields: Field A, Field B, Field C
+Default: Field B
+Position: left
+
+Parameter: text
+Widget: TextInput
+Label: Text Input
+Default: Hello, world!
+Position: right
+
+Parameter: file
+Widget: FileInput
+Label: File Input
+Default: ~/
+Position: right

inst/rmarkdown/templates/rnaseq/skeleton/README.md

@@ -0,0 +1,9 @@
+# TODO
+
+[ ] Replace Title in this file matching title projects
+[ ] run function`bcbio_set_project()` to set up information for this project
+    - hbcxxxx code
+    - pi
+    - project name to be used in storage/github/dropbox
+[ ] run function `bcbio_set_git()` to set up git repository
+[ ] run function `bcbio_copy_dropbox()` to copy files to dropbox location