Build Instructions
Build dependencies
- For APT-based systems (Debian, Ubuntu), install the following packages:
sudo apt-get install build-essential git-core cmake zlib1g-dev libncurses-dev
- For RPM-based systems (Fedora, CentOS, RHEL), install the following packages instead:
sudo yum groupinstall "Development tools"
sudo yum install zlib-devel ncurses-devel cmake
Note that for some RPM based systems (like RHEL), you will need to install cmake 2.8 or greater yourself as the packaged version is much older.
Clone the SomaticSniper repository
Clone the git repository.
git clone git://github.com/genome/somatic-sniper.git
Build SomaticSniper
SomaticSniper does not support in-source builds. So create a subdirectory, enter it, build, and run tests:
mkdir somatic-sniper/build
cd somatic-sniper/build
cmake ../
make deps
make -j
make test
The binary bam-somaticsniper can then be found under somatic-sniper/build/bin. If you have administrative rights, then run sudo make install to install the tool for all users under /usr/bin.
FAQ
I get lots of compile errors indicating that files are missing. How do I fix this?
SomaticSniper requires that it be linked to an old version of samtools (v0.1.6). This typically happens because you have attempted to link to a newer version. As of version 1.0.3, SomaticSniper includes samtools as part of its build process and you do not need to download samtools yourself.
I get errors from cmake about missing modules. How do I fix this?
As of commit 09ef624 or version 1.0.4, this should no longer be an issue and tarballs from github should function as intended. In earlier versions, SomaticSniper contained a git submodule called build-common. This submodule contains helper modules for cmake. If you downloaded the source as a tarball from github or forgot to do a recursive clone using git, then you will not have this submodule and will see cmake errors. If you are using git, we recommend you go back and use the --recursive option when cloning the SomaticSniper repository. If you cannot use git, follow the instructions below to remedy the situation.
- Download the build-common module separately here.
- Extract that tarball and rename the directory it creates to
build-common. - Replace the empty build-common subdirectory in the sniper directory with directory you just created.
- Resume following the build instructions.
I get a floating point exception on running bam-somaticsniper. What’s going on?
This has been reported when using reference fasta indexes available via the GATK resource bundle. Please try reindexing your fasta with samtools and rerunning bam-somaticsniper.