Sanitization and tidy up of Dockerfile

[ODiogoSilva]

Made some changes so that the Dockerfile better adheres the dockerfile best practices (https://docs.docker.com/engine/userguide/eng-image/dockerfile_best-practices/).

The setup of third party applications (bowtie2, bwa, etc) is no longer performed directly on /bin. Instead, temporary packages and compilations are done in /tmp/, the relevant binaries are moved to /usr/bin/ and all else is removed at the end.

Also changed final working directory to be under /home instead of /bin.

[tiagofilipe12]

This is a nice cleanup on the dockerfile. Thank you! 👍