Sanitization and tidy up of Dockerfile #4
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.
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