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I have a peripheral that has a 6 pin JST female connector that mates to the peripheral.

The other end of the cable also came with a 6 pin female JST connector that is decidedly NOT compatible with the Pi GPIO header. The first thing I did was strip off the female JST end for the Pi. I was then able to make a breadboard connection to prove out all worked and test with software.

Now my question is, for a reliable, long-term, weatherproof connection between the Pi GPIO header and this peripheral, what is my best bet for a connection? I am thinking of bringing into play a cable with weatherproof connectors Amphenol on each end, so as to ensure the peripheral can be moved with respect to the Pi itself.

For connecting to the GPIO header directly? I am almost certain directly soldering to the pins is not the way most people do it. Any tips?

How would one connect a "wire" to a Pi for the long term?

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The GPIO header is essentially an IDE hard disk connector; how about buying an IDE cable long enough to reach from Pi to the wall of the waterproof box you will use to enclose the Pi, and then solder (some of) the wires to the back of some suitable waterproof socket, look to some automotive style panel mount connector like an AT04-6P-CL06..

You've got 40 pins holding the IDE connector in place, so it should be pretty secure. If you're bothered about the flying end of the unconnected pins, could leave it in the IDE connector and just break out the wires of interest

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