Installation of breakdancer by cloning the sourcecode (and subsequent building the code) fails because the submodule "build-common" can't be cloned.
I am following the instruction from the install.MD txt file present in the breakdancer-master.zip file that can be downloaded from the breakdancer github page.
The command I use is : git clone --recursive https://github.com/genome/breakdancer.git
The error I get is :
Cloning into 'breakdancer'...
remote: Counting objects: 3493, done.
remote: Compressing objects: 100% (1504/1504), done.
remote: Total 3493 (delta 1621), reused 3403 (delta 1532)
Receiving objects: 100% (3493/3493), 2.72 MiB | 1.66 MiB/s, done.
Resolving deltas: 100% (1621/1621), done.
Submodule 'build-common' (git://github.com/genome/build-common.git) registered for path 'build-common'
Cloning into 'build-common'...
fatal: unable to connect to github.com:
github.com[0: 204.232.175.90]: errno=Connection refused
Clone of 'git://github.com/genome/build-common.git' into submodule path 'build-common' failed
The command worked fine for me. It must be an issue with a firewall or your internet connection, though sometimes the issue is on the server (github) side. I would suggest you try another machine or just try the same command again to see if you can figure out what is happening.
I'll also try to clone the project from another location.