Implemented base functionality of JEX module.

git-svn-id: svn+sshtunnel://coge.iplantcollaborative.org/storage/SVN.d/CoGe@951 aead6680-5d07-0410-860c-d65e5a4cd256
Moved the Workflow to its own seperate module.

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Added connection string and port to JEX.

git-svn-id: svn+sshtunnel://coge.iplantcollaborative.org/storage/SVN.d/CoGe@953 aead6680-5d07-0410-860c-d65e5a4cd256
Connection string now takes a host, port and returns the connection string.

git-svn-id: svn+sshtunnel://coge.iplantcollaborative.org/storage/SVN.d/CoGe@954 aead6680-5d07-0410-860c-d65e5a4cd256
Cleaned up get_status.

The get_status method does not print to stdout any more.
An additional fail status has been added when a makeflow has failed.

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Refactored add_job for a cleaner implementation.

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Added filepath option for workflow files.

git-svn-id: svn+sshtunnel://coge.iplantcollaborative.org/storage/SVN.d/CoGe@957 aead6680-5d07-0410-860c-d65e5a4cd256
Polling for complete is now more aggressive.

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Added ability for workflow to choose a log file.

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Merge branch 'JEX'

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Merge branch 'master' of github.com:LyonsLab/coge-utils