I'm new to Ubuntu, I just installed 13.04 on a dedicated machine.
I want to update to the most recent versions of scientific software namely Bowtie, Tophat and Samtools but I can't figure out how since the newer versions are not available from the software centre. These software are command line only by the way.
I'll take Bowtie as an example. I installed it from the Ubuntu Software Centre but it is an old version. I therefore downloaded the latest version from the developer's website and unzipped the pre-compiled package in my home directory. Software centre installed the old version in /usr/bin/ and some files at other locations like /usr/share/doc/ and /usr/share/man/man1/. My understanding is that having the binary in /usr/bin/ makes it available to all users and allows calling it from the command line without having to type the complete path. So, to update the software, do I overwrite the binary in usr/bin/ and the other files elsewhere with the newer versions? That seems very awkward to me. I suspect there must be some Linux command to achieve this goal but I can't find it.
Thank you all for your help.