I've successfully downloaded the CyanogenMod 10 source tree by syncing the latest repo. I've also installed the Java JDK properly and already set a ANDROID_JAVA_HOME variable but still getting those errors while executing this command "make -j4 otatools"
/bin/bash: prebuilts/gcc/linux-x86/arm/arm-linux-androideabi-4.6/bin/arm-linux-androideabi-gcc: Permission denied
/bin/bash: prebuilts/gcc/linux-x86/arm/arm-linux-androideabi-4.6/bin/arm-linux-androideabi-gcc: Permission denied
/bin/bash: prebuilts/gcc/linux-x86/arm/arm-linux-androideabi-4.6/bin/arm-linux-androideabi-gcc: Permission denied
/bin/bash: build/core/find-jdk-tools-jar.sh: Permission denied
build/core/config.mk:348: *** Error: could not find jdk tools.jar, please install JDK6, which you can download from java.sun.com. Stop.
I used these steps to register the downloaded version of Java as an alternative, and switching it to be used as the default
update-alternatives --install /usr/bin/java java /opt/jdk1.7.0_60/bin/java 1
update-alternatives --install /usr/bin/javac javac /opt/jdk1.7.0_60/bin/javac 1
update-alternatives --set java /opt/jdk1.7.0_60/bin/java
update-alternatives --set javac /opt/jdk1.7.0_60/bin/javac
Output for java -version
java version "1.7.0_60"
Java(TM) SE Runtime Environment (build 1.7.0_60-b19)
Java HotSpot(TM) 64-Bit Server VM (build 24.60-b09, mixed mode)
Output for ANDROID_JAVA_HOME
echo $ANDROID_JAVA_HOME
/opt/jdk1.7.0_60/bin/
My Machine configuration is Debian Wheezy 64 bit with 4GB RAM