...
The bottom line is that you are going to find yourself in a situation where module spider will come up empty and you're on your own to get installing a piece of software that you are dying try out installed on TACC.
Unfortunately, there is no double-click installer for TACC. Fortunately, a majority of the better and more mature programs out there (but by no means all bioinformatics software) can be fairly easily installed. If these instructions fail, you might need to find your nearest Linux guru. Or, you might try to consult Google and tinker with things a bit.
The overall steps for installing a program on a Linux system are:
...
For programs that are already compiled (converted from high level source code in a language like C into machine specific code), you are often given some choices and need to determine how to download the version that has the correct CPU architecture for your machine.
...
The website for the SSAHA2 read mapper has links to download executables compiled for several different architectures. Using commands that you have learned in earlier lessons, download the correct one to Lonestar and place it under the directory $HOME/local/bin.
| Expand | ||||
|---|---|---|---|---|
| ||||
You can often right-click to copy the URL of a link on a website and then use |
...
| Code Block |
|---|
login1$ /home1/01502/jbarrick/local/bin/ssaha2
$HOME/local/bin/ssaha2
|
Assuming you are using the bash shell, you can do this by editing your $HOME/.profile_user configuration file. This file is basically just a bash script that is run whenever you log in. You want to add a line that looks like this:
...
Important! In order to have this change take effect, you must log out or log in again to force the shell to re-read the $HOME/.profile_user file. (Alternately, you can use the command source $HOME/.profile_user one of these commands to re-read it at any time.) :
| Code Block |
|---|
. $HOME/.profile_user
source $HOME/.profile_user
|
If your path is not working or you're curious about where else your shell is looking for commands and the order, then you might want to see the value of your $PATH.
...
Warning! If you forget to include $PATH on the right side in the above example, then you will tell your shell to not look in the usual places for executables any more. This means that ls, cd, and other common commands will no longer work without typing out their whole paths, e.g. /bin/ls. This can be extremely confusing.!!
Handling multiple versions If you install a newer version of a command that is already available on TACC for yourself, then you might get confused about what version you are running when you type the command. You can see the whole path to the executable that will be run when you type a one-word command using the which command.
...
Example: Install breseq from a source code archive
breseq is a tool developed by the Barrick lab. You're going to use it in the next lesson.
breseq web page
breseq download page
breseq uses the common GNU build system install sequence. If you install other GNU tools then the same ./configure; make; make install will often be used.
| Code Block | ||
|---|---|---|
| ||
$login1 wget http://breseq.googlecode.com/files/breseq-0.17d.tar.gz $login1 tar -xvzf breseq-0.17d.tar.gz $login1 cd breseq-0.17d $login1 ./configure --prefix=$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.
For some other tools, the instructions may tell you may to skip straight to make, or you might also have to follow other instructions or install some other tools programs or libraries that the tool you want to use needs to run in addition. Generally, you can find this information in the online documentation or an INSTALL file in the root of the downloaded code.
...
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.