Scripts will be installed with package

[ryanrichholt]

As noted in #33, Following the install instructions here: https://github.com/broadinstitute/ichorCNA/wiki/Installation results in the runIchorCNA.R launcher script not being installed.

Moving the scripts into inst/ will mean they get installed with the package. Making them executable, and adding the shebang, means they can be added to the system PATH. Just add the package bin directory to your path after installing:

If you're uncertain where the package was installed you can find it with R system.file

> system.file('bin/', package='ichorCNA')
[1] "/usr/local/lib/R/3.4/site-library/ichorCNA/bin/"

Then you can that directory to your path (via .bashrc etc..), and the script can be called from anywhere:

$ export PATH="$PATH:/usr/local/lib/R/3.4/site-library/ichorCNA/bin/"
$ runIchorCNA.R -h
Usage: /usr/local/lib/R/3.4/site-library/ichorCNA/bin/runIchorCNA.R [options]
...

[jurhoades]

Thanks for the suggestion and sorry for the delayed response. Would you be able to resolve the conflicts so we can get this merged?

[ryanrichholt]

I think I've got it merged with the latest commit now. Thanks for checking it out

[ju-cheng]

HI @ryanrichholt , I tried to look for the package. The system seemed not able to locate it.

library('devtools')
Loading required package: usethis
library('ichorCNA')
system.file('bin/',package='ichorCNA')
[1] ""

[ryanrichholt]

@ju-cheng This PR was never merged, so that command will fail because the bin directory is not created when installing this package. If you search for a different item, it will probably work. For example,

> system.file('bin', package='ichorCNA')
[1] ""
> system.file('', package='ichorCNA')
[1] "C:/Users/rrichholt/Documents/R/win-library/3.6/ichorCNA"
> system.file('html', package='ichorCNA')
[1] "C:/Users/rrichholt/Documents/R/win-library/3.6/ichorCNA/html"