First, always check if the tool is already available on the server. On TACC, you can use
module spider <partoftoolname>
to check if it exists.You may need to load the biocontainers module and then type module spider <partoftoolname> to find modules that are containerized as part of biocontainer.
Installing through Conda
On the tool website, look for conda installation. Python package are parceled up as conda packages that can be installed with one command:
conda install <toolname>
Installing from Binary files
On the tool website, always look for binary files. These have already been compiled. So, you will just need to
- download the version that has been compiled for your server's operating system.
- move it to the server
- Open it (untar and/or unzip)
- Look for the executable file in the directory that is created
- Consider adding the path to the executable to your PATH variable.
Installing from Source files
Source files are the trickiest to install, although they are necessary to use whenever a program has not been compiled specifically for your version of the operating system.
Download the source file and place in a local directory (such as $HOME).
It might end with .tar.gz, and if so, run
tar -zxvf FILENAME.tar.gz
If it ends with .tar
tar -xvf FILENAME.tar
Now you should have a directory named FILENAME
cd FILENAME
Usually, there will be a README or INSTALL file that will tell you how to compile this.
The four basic commands you will usually needs to run (in order) are
./configure
make
make install
make clean
./configure
./configure will check to see if all the required packages are on your system.
When you run ./configure, you can add certain options to fine tune the install.
For instance
./configure FILENAME --prefix=$HOME/bin
would put the executables in /opt rather than the default (usually /usr/local).
You can list the possible options with
./configure --help
The configure command will usually tell you what it is lacking, but you'll need to run it again and make sure it runs cleanly before you go on the next step.
make
Make compiles the code using the options you specified with the configure command.
At this point you will get errors pertaining to the options you specified.
make install
The make install command actually installs the code.
make clean
This optional step deletes any temporary files created during the install.
Alteratively, they may provide a setup bash or python script and you will need to run it.
Again, look for options such as --user, --prefix to set up the software in your local directory instead of a directory you don't have write permissions to.
Once installed, consider adding the installed executable to your PATH variable.
