Learning from planemo's cookiecutter template here.

 - Add Makefile at top-level.
 - Auto-generate modules, etc...
 - Place docs right in docs/ instead of docs/source.

flake8 calls it internally anyway.

 - Imports must come before everything else now.
 - Cannot assign lambda to vars - boo!

Remove escaping of quotes in the slurm cli status checks, I don't think they should be there (the format args should in fact be quoted).

update link to job managers documentation

Should make pulsar.readthedocs.org significantly prettier (all changes stolen from planemo which was generated from cookiecutter).

Replace all LWR references with Pulsar references

Refactored to check if SSH key exists, in the rare event that it has stopped existing sometime during the transfer

Handle unlinking of SSH key instead of relying on tempfile

Perhaps it's a version/environment difference, but relying on tempfile to
unlink the file when done seems to not be working. I imagine it is because
tempfile unlinks the handle when I called f.close(), so we're just going to
handle unlinking ourselves and solve that problem permanently. This has the
added benefit of us knowing that the file will be removed as soon as the
transfer is complete. RSA keys on disk for a smaller amount of time "feels"
better.

Typo of pubkey PreferredAuth options

Removed unused logging and centralized SSH options

SSH options are used the same in each section of the config, thus it makes sense to
set them once and re-use in each command requiring those arguments.

Redact password in connection URL, Fixes #36

Largely stolen from planemo's which in turn was prepolated using cookiecutter (https://github.com/audreyr/cookiecutter).

SSH Transport Implemented

Galaxy file_actions.yaml:

    paths:
        - path: /home/vagrant/
          action: remote_scp_transfer

Behaves identically to rsync

Provides the file action "remote_rsync_transfer". This currently
*requires* you to use a `file_action_config` on the Galaxy side, as
extra configuration is required.

Galaxy job_conf.xml:

    <destination ...>
        <param id="file_action_config">file_actions.yaml</param>

Galaxy file_actions.yaml:

    paths:
        - path: /home/vagrant/
          action: remote_rsync_transfer
          ssh_user: vagrant
          ssh_host: my.fqdn
          ssh_port: 2222
          ssh_key: |
            -----BEGIN RSA PRIVATE KEY-----
            MIIEowIBAAKCAQEAwWYGEOhiJgbWv8eBV2LJp0MCSgrAPeX9FbsGn1I+UC110PPW

This passes configuration information in every message to Pulsar. While
suboptimal in terms of message size (ssh key is ~3x the size of a normal
message), it opens the door to multiple galaxies connecting to a single pulsar,
still using rsync. Additionally it lets the Galaxy admin reconfigure the SSH
parameters without any interaction on the Pulsar admin's part (with the
exception of `ssh_key`, as of now). This will be very beneficial if the two
groups do not have a close working relationship.

Added MQ tutorial/intro and linked docs