cellID-linux

This is meant to aid compilation of cellID v1.4 in GNU/linux systems.

There is also VCellID, a friendlier and more automated graphical user interface for Cell-ID.

I became tired of fighting with unincluded dependencies, and so tried autotools by following this tutorial and using other web resources. It was useful to understand the code, and further resources can be found in the comments within the configure.ac and Makefile.am files, explaining each line.

Credits

The cellID developers (1)(2).

The original source can be found at sourceforge (link) and in the original publication (link).

Dependencies

Ubuntu

Disclaimer: it is possible that not all of the installed packages are strictly required. I have not yet checked, but surely the "-dev" ones are essential in Ubuntu.

I have made use of autotools, and have installed the following packages:

• automake: 1:1.15-4ubuntu1
• autoconf: 2.69-9
• libtool: 2.4.6-0.1

You may install these in Ubuntu systems by running:

sudo apt-get install automake autoconf libtool

The configure.ac and Makefile.am files have been set to require libtiff5-dev, libopenlibm-dev, and libglib2.0-dev.

• libglib2.0-dev: 2.48.2-0ubuntu1
• libtiff5-dev: 4.0.6-1ubuntu0.4
• libopenlibm-dev: 0.5.0+dfsg-2

You may install these in Ubuntu systems by running:

sudo apt-get install libglib2.0 libglib2.0-dev libtiff5 libtiff5-dev libopenlibm-dev

Arch

These dependencies can also be satisfied in Arch Linux, sorry for not providing detailed instructions. I got openlibm from AUR, the rest are provided by standard repos.

sudo pacman -S automake autoconf libtool glib2 libtiff

aurman -S openlibm OR yay -S openlibm

Notes

You may find details on how the automake/conf files are configured by opening them and reading the comments.

Surprisingly for me, packages may be installed using one name (such as libtiff5) but configure.ac can find them using another one (such as libtiff-4).

Build and Install

To build and install, please cd into the directory where the files are and run:

autoreconf -fvi
./configure
make -j8
sudo make install

Please refer to the cellID documentation to learn how to use this program.

Cheers!

Usage

Parameters

$ cell -p parameters.txt

Example parameters are in the parameters_example.txt file, and a full description is available in parameters_description.txt (copied from Gordon et. al. 2007).

Run cell --help-all for commandline help.

Output

For convenience, I have copied the out_all columns' description to output_descriptions.csv.