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:
  1. $ sudo mkdir /usr/local/include/bamtools-for-SGA
  2. $ sudo ln -s /usr/local/include/bamtools/ /usr/local/include/bamtools-for-SGA/include
  3. $ 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:
  • pysam (http://code.google.com/p/pysam/)
  • ruffus (http://www.ruffus.org.uk/)

Installation

1. $ cd /programinstallers/
2. $ git clone https://github.com/jts/sga.git
3. $ cd sga/src
4. $ ./autogen.sh
5. $ ./configure --with-bamtools=/usr/local/include/bamtools-for-SGA --with-hoard=/usr/lib64
   Google sparsehash was detected automatically
6. $ make
7. $ make install
8. $
9. $
10. Cleanup
    $ cd /programinstallers
11. $ rm sga -rf