PALM — Pemutation Analysis of Linear Models — uses either MATLAB or Octave behind the scenes. It can be executed from within either of these environments, or from the shell, in which case either of these is invoked, depending on how PALM was configured.

For users who do not want or cannot spend thousands of dollars in MATLAB licenses, Octave comes for free, and offers quite much the same benefits. However, for Octave, some functionalities in PALM require version 4.4.1 or higher. However, stable Linux distributions such as Red Hat Enterprise Linux and related (such as CentOS and Scientific Linux) still offer only 3.8.2 in the official repositories at the time of this writing, leaving the user with the task of finding an unofficial package or compiling from the source. The latter task, however, can be daunting: Octave is notoriously difficult to compile, with a myriad of dependencies.

A much simpler approach is to use Flatpak or Snappy. These are systems for distribution of Linux applications. Snappy is sponsored by Canonical (that maintains Ubuntu), whereas Flatpak appears to be the preferred tool for Fedora and openSUSE. Using either system is quite simple, and here the focus is on Flatpak.

To have a working installation of Octave, all that needs be done is:

1) Make sure Flatpak is installed:

On a RHEL/CentOS system, use (as root):

yum install flatpak

For openSUSE, use (as root):

zypper install flatpak

For Ubuntu and other Debian-based systems:

sudo apt install flatpak

2) Add the Flathub repository:

flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo

3) Install Octave:

flatpak install flathub org.octave.Octave

4) Run it!

flatpak run org.octave.Octave

Only the installation of Flatpak needs be done as root. Once it has been installed, repositories and applications (such as Octave, among many others) can be installed at the user level. These can also be installed and made available system-wide (if run as root).

Configuring PALM

From version alpha117 onwards, the executable file ‘palm’ (not to be confused with ‘palm.m’) will include a variable named “OCTAVEBIN”, which specifies how Octave should be called. Change it from the default:

OCTAVEBIN=/usr/bin/octave

so that it invokes the version installed with Flatpak:

OCTAVEBIN="/usr/bin/flatpak run org.octave.Octave"

After making the above edits, it should be possible to run PALM directly from the system shell using the version installed via Flatpak. Alternatively, it should also be possible to invoke Octave (as in step 4 above), then use the command “addpath” to specify the location of palm.m, and then call PALM from the Octave prompt.

Octave packages

Handling of packages when Octave is installed via Flatpak is the same as usual, that is, via the command ‘pkg’ run from within Octave. More details here.