SPECX can be run in batch mode, as long as you don't ask it to display spectra on the terminal or anything like that. The following DCL command file reads all channel B spectra from the file OBS_RXC_0129.DAT into the currently open map. It can be submitted in the usual way, using the DCL SUBMIT command.
$ assign sys$command sys$input
$ assign disk$data:[rachael.specx] sys_specx
$ @sys_specx:specxstart
$ set default mydata
$ specx/map=S140_ci_0129b
set-dump n
set-gsd-filename 'obs_rxc_'
interactive = false
replace = true
map_tol = 0.75
read-gsd-map 2 \ 129 \ ^z
exit
$ exit