This page was last updated on Wednesday, 16-Jul-2014 15:36:04 CDT
Installation notes for SGA - String Graph Assembler version 0.10.13
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Prerequisites
- google sparse hash library
(http://code.google.com/p/google-sparsehash/)
- the bamtools library
(https://github.com/pezmaster31/bamtools)
The configure file will not allow specification of library and headers separately,
so an easy way to trick it is with two symlinks:
- $ sudo mkdir /usr/local/include/bamtools-for-SGA
- $ sudo ln -s /usr/local/include/bamtools/ /usr/local/include/bamtools-for-SGA/include
- $ sudo ln -s /usr/local/lib/bamtools /usr/local/include/bamtools-for-SGA/lib
- zlib
(http://www.zlib.net/)
- (optional but suggested) the jemalloc memory allocator
(http://www.canonware.com/jemalloc/download.html)
- Additionally, the pipeline python scripts use the following modules. These
are not required to build SGA but must be available if you want to use the relevant
python helper scripts:
Installation
- $ cd /programinstallers/
- $ git clone https://github.com/jts/sga.git
- $ cd sga/src
- $ ./autogen.sh
- $ ./configure --with-bamtools=/usr/local/include/bamtools-for-SGA --with-hoard=/usr/lib64
Google sparsehash was detected automatically
- $ make
- $ make install
- $
- $
- Cleanup
$ cd /programinstallers
- $ rm sga -rf