galaxy: Make a function available in Galaxy

In RGalaxy: Make an R function available in the Galaxy web platform

Description

Makes an R function available in the Galaxy web platform. Automates all the work necessary to expose an R function in Galaxy. See the vignette for more information

Usage

galaxy(func, 
        package=getPackage(func),
        manpage=func, 
        name=getFriendlyName(func),
        version=getVersion(func),
        galaxyConfig,
        dirToRoxygenize,
        RserveConnection=NULL,
        path.to.R="",
        functionalTestDirectory)

Arguments

func	Required. TA character vector naming the function to make available in Galaxy. This function should be entirely-self contained, and should accept as arguments the full paths to its input and output file(s).
package	The name of the package where func lives, or NULL if it is not in a package. By default, RGalaxy will try to determine which package the code lives in and set the parameter to NULL if it cannot.
manpage	The full path to the Rd-formatted manual page for the function, or if the func is in a package, an alias that will pull up that manpage.
name	Text describe the action this function performs. Becomes a clickable link in Galaxy. By default, if your function is called "fooBar", name is set to "Foo Bar".
version	The version of this function. If func lives in a package, defaults to the version of package.
galaxyConfig	Required. A link{GalaxyConfig} object describing your Galaxy configuration.
dirToRoxygenize	If present, points to the directory of a source package upon which to run roxygenize() from the roxygen2 package, creating manual pages from source code comments.
RserveConnection	If set (by calling RserveConnection), sends the function to a running Rserve for evaluation. This can make functions run faster since dependencies have already been loaded. If NULL (the default), function is run normally. See vignette for more information.
path.to.R	If not empty, Galaxy will look for R in this directory. This is useful if there are multiple versions of R on your system and your Galaxy configuration prevents you from setting your PATH to point to the right one.
functionalTestDirectory	If package is not specified, this directory is searched for functional test fixtures.

Value

invisible(NULL)

See Also

GalaxyConfig, GalaxyOutput, GalaxyParam

Examples

## set up galaxyHome (you don't need to do this if 
## you really have Galaxy installed)
galaxyHome <- tempdir()
dir.create(galaxyHome, recursive=TRUE, showWarnings=FALSE)
file.copy(system.file("galaxy", "tool_conf.xml", package="RGalaxy"),
    file.path(galaxyHome, "tool_conf.xml"), overwrite=FALSE)

## Not run: 
galaxy("functionToGalaxify",
    galaxyConfig=GalaxyConfig(galaxyHome, "mytool",
      "Test Section", "testSectionId"),
    RserveConnection=RserveConnection())

## End(Not run)

Example output

Loading required package: XML
Loading required package: tools

Attaching package: 'tools'

The following object is masked from 'package:XML':

    toHTML

Loading required package: optparse
Loading required package: digest
[1] TRUE
Loading required package: RSclient
[1] "/work/tmp/tmp/Rtmpt9HUFK/tools/mytool/functionToGalaxify.xml"
Warning messages:
1: In dir.create(testDataDir) :
  cannot create dir '/work/tmp/tmp/Rtmpt9HUFK/test-data/functionToGalaxify', reason 'No such file or directory'
2: In file.create(to[okay]) :
  cannot create file '/work/tmp/tmp/Rtmpt9HUFK/test-data/functionToGalaxify', reason 'No such file or directory'
3: In file.create(to[okay]) :
  cannot create file '/work/tmp/tmp/Rtmpt9HUFK/test-data/functionToGalaxify', reason 'No such file or directory'
4: In file.create(to[okay]) :
  cannot create file '/work/tmp/tmp/Rtmpt9HUFK/test-data/functionToGalaxify', reason 'No such file or directory'
5: In file.create(to[okay]) :
  cannot create file '/work/tmp/tmp/Rtmpt9HUFK/test-data/functionToGalaxify', reason 'No such file or directory'

RGalaxy documentation built on Nov. 8, 2020, 7:42 p.m.