sortchannel.m

function sortchannel()

if(isempty(dir('skipsort.txt')))
	% get channel string
	[p1, chstr] = nptFileParts(pwd);
	% get array string
	[p2, arrstr] = nptFileParts(p1);
	% get session string
	[p3, sesstr] = nptFileParts(p2);
	% get day string
	[p4, daystr] = nptFileParts(p3);
	
	% make channel direcory on HPC, copy to HPC, cd to channel directory, and then run hmmsort
	display('Creating channel directory ...')
	syscmd = ['ssh eleys@atlas7 "cd ~/hpctmp/Data; mkdir ' daystr '; cd ' daystr '; mkdir ' sesstr '; cd ' sesstr '; mkdir ' arrstr '; cd ' arrstr '; mkdir ' chstr '"'];
	display(syscmd)
	system(syscmd);
	display('Transferring rplhighpass file ...')
	syscmd = ['scp rplhighpass.mat eleys@atlas7:~/hpctmp/Data/' daystr '/' sesstr '/' arrstr '/' chstr];
	display(syscmd)
	rval=1;
	while(rval~=0)
		rval=system(syscmd);
	end
	display('Running spike sorting ...')
	syscmd = ['ssh eleys@atlas7 "cd ~/hpctmp/Data/' daystr '/' sesstr '/' arrstr '/' chstr '; ~/hmmsort/hmmsort_pbs.py ~/hmmsort"'];
	display(syscmd)
	system(syscmd);
end