Origin/new config

[leeprichman]

• update install script, README, and code to support external netMHC dependencies
• added function to configure netMHC scripts, correctly add to $PATH
• test updates to ignore version dependent differences in netMHC (alleles, predictions etc)
• new tcsh dependency in install script

[andrewrech]

(?i)

On Dec 3, 2019, at 4:37 PM, Lee Richman notifications@github.com wrote:

@leeprichman commented on this pull request.

In R/antigen.garnish_run.R:

• on.exit({setwd(owd)})

• netMHC parent dir in ag data dir

• npd <- file.path(dir, "netMHC")
• if (!dir.exists(npd)) dir.create(npd)

• get path to scripts

• setwd(npd)
• tool_paths <- list.files()
• f <- lapply(tool_paths, function(i){

• this pattern could one day break.

• list.files(i, pattern = "netMHC(II)?(pan)?-?([0-9]\.[0-9])?$",

is there a better way than just [Nn][Ee][Tt][Mm] etc? if not will do that.

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