I'll be the first to say that I am a linux noob,  the one step that held me up was installing the libraries.  These might not be entirely right but its from memory, and remember I am very new to linux but I'll try to help.  I am using Raspbian.

To install cpuminer:

Terminal root:
 sudo apt-get update
 sudo apt-get install build-essential libtool libcurl4-openssl-dev libncurses5-dev libudev-dev autoconf automake
 git clone https://github.com/gridseed/usb-miner
 cd /home/pi/usb-miner/software/cpuminer
 sh ./autogen.sh
 sh ./configure
 make && make install

 [wait till done installing, then plug in you usb miners]
 dmesg
 [find and copy down the names of your USB miners,  they should look like (ttyUSB0) and so on.  
 sudo nano /home/pi/usb-miner/software/cpuminer
[this is a text editor]
 minerd --freq=850 -G /dev/ttyUSB[Number for usb device] [if more then one miner write -G before each] --url= [poolurl:port] --userpass=[user].[worker]:[password]  
[CTRL+X]
[Y]
[name the file [whatevername.sh]
 
Now run the file that you just saved.

sh ./[name of file .sh]


Should be off to the races unless I missed some step above, I am a noob but with the help from others I figured it out, this if for CPUminer which you can run scrypt pools.  Need cgminer installed to run SHA-256 coins, which is also in the software folder you downloaded.  If when trying to compile you get an error like missing lib something, type ldconfig while in the directory.

EDIT: There is also a installation how to in the https://github.com/gridseed/usb-miner/tree/master/software/doc , folder.