Change README to reduce redundancy.

genome · Jul 15, 2015 · 753681e · 753681e
1 parent 23ce070
commit 753681e
Showing 1 changed file with 6 additions and 64 deletions.
diff --git a/README.md b/README.md
@@ -2,71 +2,13 @@
 
    The purpose of this program is to identify single nucleotide positions that are different between tumor and normal (or in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the differences. Complete documentation is available at the project [web site](http://gmt.genome.wustl.edu/somatic-sniper/) or in the included [pdf](https://github.com/genome/somatic-sniper/blob/master/docs/sniper_manual.pdf).
 
-## Build Dependencies
+## License
+SomaticSniper is licensed under the [MIT license](docs/copyright). 
 
-* git
-* cmake 2.8+ ([cmake.org](http://cmake.org))
-
-## 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
-
-Recursively 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](https://github.com/genome/somatic-sniper/releases/tag/v1.0.3), 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](https://github.com/genome/somatic-sniper/commit/09ef624e5bb275e0fd62396a14a878711e746cb9) or version [1.0.4](https://github.com/genome/somatic-sniper/releases/tag/v1.0.4), 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.
-
-1. Download the build-common module separately [here](https://github.com/genome/build-common/tarball/master).
-2. Extract that tarball and rename the directory it creates to `build-common`.
-3. Replace the empty build-common subdirectory in the sniper directory with directory you just created.
-4. 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`.
+## Documentation
+* [Installation](gmt/install.md)
+* [Usage](gmt/documentation.md)
+* [FAQ](gmt/install.md#faq)
 
 ## User Support