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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 the a piece of software that you are dying to run 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 readily installed in a few similar waysfairly easily installed.
The overall steps for installing a program on a Linux system are:
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Note: Most Linux installs will work similarly on MacOSX, with just a few additional preambles (install XCode, maybe some extra libraries, etc). With much more extra work, it is possible to set up a Linux-like environment in Windows as well. Both of these topics are outside the scope of what we are going to cover here.
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You can get your CPU architecture with this command:
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login1$ arch |
Output might be something like i386 (for my MacBook) or x86_64 (for Lonestar).
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The website for the SSAHA2 read mapper has links to download 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.
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You can often right-click to copy the URL of a link on a website and then use |
How the shell finds executables: $PATH
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Assuming you are using the bash shell, you can do this by editing your $HOME/.profile_user configuration file. This configuration file is basically just a bash script that is run whenever you log in. You want to add a line that looks like this:
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export $PATHPATH="$HOME/local/bin:$PATH" |
This sets the environmental variable PATH to point to its old value with your new directory appended to the front (the : separates multiple paths). This means the shell will look for executables in this new location first, then it will look in all of the standard locations after that. For more information on environmental variables see the Bash Beginner's Guide.
Important! In order to have this change take effect, you must log out or log in again to force the shell to re-read the ~$HOME/.profile_user file. (Alternately, you can use the command source ~$HOME/.profile_user to re-read it at any time.)
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login1$ echo $PATH login1$ env |
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For some other tools you may skip straight to make or have to follow other instructions or install some other tools 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.Finally, remember to
Other Cases
In other lessons we'll cover various deviations and elaborations on these two procedures in order to install specific programs.