Punch or drill a small hole in the top or bottom of the clamshell for the cable to pass through while the case is completely zipped, or just run the cable out where the zipper ends. Like zip it 99% of the way closed leaving room for the cable to exit.
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This is how many backpacks work. 
Theres not a second zipper on the other side to seal it tho
I see, Iβm not sure I understand your post then.
Get a longer USB cable, run it out the base of wherever the zipper is, and up the outside of the case?
Any way to tie it with a pipe cleaner?
Looks like you could just flip the drive so the ports are at the top where the zipper ends.
I wouldn't use it heavily while it's enclosed inside the case. You may run into thermal issues.
After looking at the picture a little closer, thereβs not much room in that case for the rigid portion of the USB connector when itβs plugged in. I think your best bet would be flip the drive so the USB port is facing up (towards the end of the zipper) and plug in the cable and zip the case like 80-90% closed. Good luck!
Since it's a one-way zipper you probably have to bring some of the cord around the inside to the end and zip to there. If you're worried it will unzip you can possibly use a safety pin π§· across the zipper behind the pull.
First, heat will be a concern of it's plugged in for any length of time - the zippered case will act like an insulator.
If you're still set on doing this, you can either orient the drive so the cables protrude from the closing end of the zipper, or poke holes through the case in a spot that's ideal.
That kind of material tends to fray when cut, but melting a hole with a soldering iron works well-it seals the edge.
If space in there is limited, or you want to have the cables routed differently, there are 90Β° cables/adapters which can help.

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