INSTALL

Welcome to DWGSIM

=== Prerequisites ===

If you have just cloned this repository using GIT, you must 
initialize the SAMtools sub-module:
 git submodule init
 git submodule update
You should now have the SAMtools-compatible version checked
out in the samtools sub-directory.

=== Building DWGSIM ===

To build DWGSIM, execute the following commands:
 make

To install DWGSIM, after building, copy the following binaries
to their appropriate installation directories:
 dwgsim
 dwgsim_eval
 dwgims_pileup_eval.pl

=== DWGSIM with Galaxy ===

DWGSIM can be incorporated into galaxy.
NB: this is out-of-date.

1. Copy over the wrapper scripts:
  cp scripts/galaxy/dwgsim_wrapper.* galaxy-dist/tools/sr_mapping
2. Add to the list of available tools.
  2a. Open galaxy-dist/tool_conf.xml 
  2b. At the end of the NGS: mapping section, add the following:
    <tool file="sr_mapping/dwgsim_wrapper.xml" />