Additional Dependencies (optional)
Setting up a conda environment
Conda is an incredibly convenient tool to keep all packages and tools used by expam in the same place, isolating it from all other tools on your computer.
See here for instructions on how to install Conda. Conda searches online repositories for the software you ask it to install. There are certain repositories you should let Conda know about, which contain a lot of useful bioinformatics software.
$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
We now create the conda environment, and call it expam.
$ conda create --name expam python=3.8
You enter the environment using conda activate, at which point your console will indicate
you are in an environment by adding (expam) to the start of each line. All applications
installed using Conda from within this environment will only be accessible upon entering
the environment. You can leave the environment using conda deactivate.
$ conda activate expam
(expam) $ conda list
# packages in environment at /opt/anaconda3/envs/test:
#
# Name Version Build Channel
ca-certificates 2021.10.8 h033912b_0 conda-forge
libcxx 12.0.1 habf9029_0 conda-forge
libffi 3.4.2 h0d85af4_5 conda-forge
libzlib 1.2.11 h9173be1_1013 conda-forge
ncurses 6.2 h2e338ed_4 conda-forge
openssl 3.0.0 h0d85af4_2 conda-forge
pip 21.3.1 pyhd8ed1ab_0 conda-forge
python 3.8.12 h43ca1e7_2_cpython conda-forge
python_abi 3.8 2_cp38 conda-forge
readline 8.1 h05e3726_0 conda-forge
setuptools 59.1.1 py38h50d1736_0 conda-forge
sqlite 3.36.0 h23a322b_2 conda-forge
tk 8.6.11 h5dbffcc_1 conda-forge
wheel 0.37.0 pyhd8ed1ab_1 conda-forge
xz 5.2.5 haf1e3a3_1 conda-forge
zlib 1.2.11 h9173be1_1013 conda-forge
(expam) $ conda deactivate
$
Additional Software
If you wish to build your own tree for a custom collection of genomes using the expam interface, you will need some tools. See Tutorial Three for a tutorial on how to build trees using the expam interface, this should make you aware of which software you will need. Brief instructions for installing all possible software are shown below.
Note: whenever the tutorials mention a ‘local installation’ of some tool, this simply means that the tool should be available from a call in the console. Installing any required tools within the environment using the following commands will satisfy this.
Installing Mashtree
Mashtree requires a local installation of mash. Run the following commands in succession.
$ conda install mash
$ conda install mashtree
Installing Mash
$ conda install mash
Installing RapidNJ
$ conda install rapidnj
Installing QuickTree
$ conda install quicktree