Being a gun line Tau player I have a few different ways I deal with Jump Infantry (mainly Assault Marines and Death Company). This is mostly for shooting armies.
1. If they are advancing across the board try to get an angle on them. If you can reach them around the cover, you can get another round or two of firing. If Jump Infantry, or any assaulting unit, fails to reach your line on the charge then you can either rapid fire at them or you can get the charge in. On this note, if you know that you will be facing an assault focused army with a shooting army make sure there are at least 18" between you and a concealing piece of terrain.
2. Make sure you have a reaction force. Jump infantry can deep strike behind your lines and tie up your fire support or get into your line. Have someone, for me crisis suits, near your lines so you can stop them before they can assault you.
There are some things, for instance vanguard veterans and death company dreadnoughts in drop pods, that can assault without being shot at most of the time. If you have a fire base or gun line style and get hit with one of these you can counter assault into the melee with any nearby assault based units.
If you don't you can make a much more cinematic end to the assaulting unit. If you have, say 10 Terminators with a chaplain hit your line, just march your troops into rapid fire range. Remember, they can't consolidate into you. Then you can kill them with the rest of your troops rapid firing into them.
That which doesn't kill me has made a tactical mistake.
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