New all-in-one script, run_snp_pipeline.sh
Fix run_snp_pipeline usage
Fix errors in documentation.
Fix problems with Mac compatibility.
Consistent logging for both torque and workstation runs.
Added Listeria dataset and documentation to package.
Merge remote branch 'origin/master'
Added in sha256sumCheck that I forgot to copy over.
Add file freshness checks and force flag to python scripts.
Merge remote-tracking branch 'origin/master'
Changes for distributing the listeria data set.
Changes for distributing the listeria data set.
Merge branch 'master' of /home/steven.davis/mnt/biob/svn/Biostats/rand/repo/snppipeline
Update the link to the associated paper on peerj.
* Changes to use configuration file parameters.
* Added a machine-generated command reference help page.
* Document new functionality for the next release.
* Changed scripts to check for empty files as part of freshness checks.
Comment code
Clarify usage when rebuilding into a different output directory.
Merge remote-tracking branch 'origin/master'
Update data dir readme