agalma /



Agalma is optimized to run on one node with at least 8 cores and a large amount of RAM. The RAM should be about one and a half times as large as your input files.

Software dependencies:

Please follow the INSTALL instructions for BioLite before these instructions.

Installing from the tar ball

Unpack the tarball (from

tar xf agalma-X.X.X.tar.gz
cd agalma-X.X.X

Run the configure script (use -h to see the available options):


After configuring, install with:

sudo make install

This installs Agalma to /usr/local by default. If you would like to install to a location other than /usr/local (if you don't have permission to write to /usr/local, for example), see the "Installing to an alternative location" section.

Proceed to "Installing BLAST databases"

Installing from the git repo

(Skip this unless you are building a development version that you cloned from Bitbucket.)

First, create a fork of the agalma repository so that you can later send a pull request so that we can incorporate your improvements. Then clone your forked repository.

You will need to have the automake, autoconf and libtool packages installed. To produce the configure scripts, use the command:


Then you can use the typical build sequence:

sudo make install

Proceed to "Installing BLAST databases"

Installing BLAST databases

To download and install BLAST databases that have been optimized for use with Agalma, run the command:

agalma blastdb

You may need to prefix this command with sudo if you installed Agalma to a location that you don't have access write to (like /usr/local).

Follow the instructions in TUTORIAL to test your installation and see how to use Agalma.

Installing to an alternative location

The instructions above assume that you are installing Agalma to /usr/local, which requires root access. If you are installing to another location, modify the installation instructions as follows. These are not full instructions, they just explain how to modify the instructions above.

In the instructions below, we use [installation_path] as a placeholder for the path that you would like to install to, e.g. /home/lucy/local. Note that [installation_path] needs to be an absolute path.

Modify the configure command to changethe install location:

./configure --prefix=[installation_path]

Proceed to the instructions below for setting paths, then with make and make install.

Setting PATH

If you install to a canonical location on your system, like /usr/local, the agalma script will already be in your PATH. Otherwise, you need to add the new bin directory to your PATH so that you can call agalma. In bash (you can add add this to ~/.bashrc):

export PATH=[installation_path]/bin:$PATH

or in csh:

setenv PATH [installation_path]/bin:$PATH

Note that if you are installing at the same alternate location used by BioLite, the directory may already be in your path.

Generating a tarball from the git repo

You can generate a tarball with the commands:

make dist-gzip