Merge branch 'irwin-taxon_filter' into irwin-tool_enhancements
In tools/__init__.py, set __all__ to automatically contain all tools. Check return from os.system in post_download.
tweak to check
Merge pull request #16 from broadinstitute/irwin-tool_enhancements

Made changes to DownloadPackage and got rid of DownloadScript, handle bz2 compression in DownloadPackage, added post_download_command argument to DownloadPackage, a command that will be executed in the destination directory, created tools for samtools and picard.
basic install method for bwa
basic execute for bwa
create install methods before trying to append to is
separate subcommand into own argument
fix jenky spacing in bmtagger, as tests seem to fail there
[hml-bwa] changed parenthesis type to hopefully fix string formatting
Added additional debugging and info statements to package downloader.  Working bwa download and installation.  Some retabbing of tools/__init__.
use exec_path insted of BWA_DIR.  some documentation. use python style string formatting instead of c style string formatting
pull request changes
Moved ebola.fasta from TestLasta folder to general input folder, and made appropriate adjustments to tests already using the file.  Added test case for "bwa index".
Resolved issue #20 by adding post_download_ret argument to DownloadPackage.
Merge pull request #21 from broadinstitute/irwin-issue20

Resolved issue #20 by adding post_download_ret argument to DownloadPacka...
Added bwa aln test + ability to specify some commandline argument to dirrectly follow bwa to allow for pipes and dirrecting output
Merge branch 'master' of github.com:broadinstitute/viral-ngs into hml-bwa
fixed spacing/tab issue in file.py
fix python 2 to 3 encoding compatiblity issue