install binary asset during installation of jgi pipeline

Link: https://github.com/kbase/assembly/issues/50
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
move the executable in assets during the installation

Link: https://github.com/kbase/assembly/issues/50
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
add patch for the JGI rolling QC pipeline

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
apply a patch before moving product content

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
fix prefix count for patching

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
patch os_utility2

Link: https://github.com/kbase/assembly/issues/50
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
Merge pull request #65 from sebhtml/issue-26

Issue 26
add standalone makefile
add abs_path tool for the standalone deployment to work on mac
fix standalone deployment path
add the wait option for the client get command:
ar-run ... | ar-get -w -a --stdout | annotation-commands
add ar-filter command (to be merged into ar-get)
move filtering options to ar-get
Merge pull request #66 from levinas/master

standalone deployment, wait option and filtering contigs by length