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$login cdw
$login wget ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_v2.5.5_x86_64.tgz
$login tar -xvzf ssaha2_v2.5.5_x86_64.tgz
$login cd ssaha2_v2.5.5_x86_64
$login mkdir -p $HOME/local/bin
$login mv ssaha* $HOME/local/bin

How the shell finds executables: $PATH

Now, you might want to tell your login shell that it should look for executable files in this new directory $HOME/local/bin. This will allow you to use the executable as a one-word command like you are used to:

login1$  ssaha2

Instead of writing out the entire path to the executable to run it, like in one of these examples:

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breseq uses the common GNU build system install sequence. If you install other GNU tools then the same ./configure; make; make install command sequence will often be used.

$login1 cdw
$login1 wget http://breseq.googlecode.com/files/breseq-0.17d19.tar.gz
$login1 tar -xvzf breseq-0.17d19.tar.gz
$login1 cd breseq-0.17d19
$login1 ./configure --prefix=$HOME/local
$login1 make
$login1 make install

The extra option --prefix to ./configure sets where the executable and any other files associated with the program will be installed. If you leave off this flag, then it will try to install them in a system-side location. You must have administrator privileges to do this and would generally have to substitute sudo make install for the last step to get this to work. That won't work on TACC! (sudo means "super-user do".)

For some other tools, the instructions may tell you to skip straight to make, or you might also have to install some other programs or libraries that the tool you want to use needs to run. Generally, you can find this information in the online documentation or an INSTALL file in the root of the downloaded code.

Other Cases

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More Examples

Example: Install the latest version of Bowtie2

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Other Cases

In other lessons we'll cover various deviations and elaborations on these two procedures in order to install specific programs, R modules, Perl modules, Python modules, etc.