A docker image for this software can be found at https://hub.docker.com/r/jwirth/phantasm
Automating microbial taxonomy workflows with PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
Joseph S. Wirth & Eliot C. Bush, 2023
doi: 10.1093/nar/gkad196
Note: PHANTASM requires an email address for communicating with NCBI as described in python's Bio.Entrez package. The email address is not stored or used for any other purposes.
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1.3. Native Installation
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3.1. External software
3.2. Python modules
3.3 R packages
The easiest way to get started is is to use the Docker image. There are instructions for using phantasm as a Docker container on dockerhub. The Docker image contains all of the dependencies pre-installed and only requires that Docker Desktop is installed (or docker if using a linux server). Alternatively, Singularity may be used. Please see the detailed tutorial for using a PHANTASM in a container for more information.
To install phantasm using conda, run the following commands:
conda config --add channels bioconda
conda install phantasm
Instructions for running phantasm within a conda environment are identical to those for the Docker image. See the detailed tutorial for more information.
PHANTASM requires python3 (v. 3.9+). This can be installed via the command line with the following command:
sudo apt-get -y install python3.9 python3-pip python3-setuptools python3-dev
mummer is needed for calculating ANI using pyani. It can be installed with the following command:
sudo apt-get -y install mummer
curl is necessary for certain R libraries to function properly. It can be installed with the following command:
sudo apt-get -y install curl libcurl4-openssl-dev
blast+ is required for calculating core genes and average amino acid identity. It can be installed with the following command:
sudo apt-get -y install ncbi-blast+
R needs to be installed for plotting heatmaps of the overall genome-related indices. It can be installed with the following command:
sudo apt-get -y install r-base
The following R libraries need to be installed: ape, gplots, dendextend, and BiocManager. It also needs the DECIPHER bioconductor package. These can be installed using the following commands. Warning: These packages can take several minutes to install.
R -e "install.packages('ape',dependencies=TRUE, repos='http://cran.rstudio.com/')"
R -e "install.packages('gplots',dependencies=TRUE, repos='http://cran.rstudio.com/')"
R -e "install.packages('dendextend',dependencies=TRUE, repos='http://cran.rstudio.com/')"
R -e "install.packages('BiocManager',dependencies=TRUE, repos='http://cran.rstudio.com/')"
R -e "BiocManager::install('DECIPHER')"
The following python packages need to be installed: numpy, scipy, Bio, textdistance, parasail, rpy2, pyani. They can be installed with pip3 using the following commands:
pip3 install scipy
pip3 install Bio
pip3 install textdistance
pip3 install numpy
pip3 install parasail
pip3 install rpy2
pip3 install pyani
PHANTASM requires FastTree (or FastTreeMP), [muscle v5.1](MUSCLE v5.1), and iqtree v1.6.12 to be installed. It also needs the source code for xenoGI v3.1.2.
Finally, clone the PHANTASM repository or download a release.
In order for PHANTASM to function properly, you will need to modify the file param.py found in the phantasm directory. Specifically, you need to modify the following fields as shown in the table below:
_______________________________________________________________________
| variable name | variable value |
|---------------|-------------------------------------------------------|
| BLASTPLUS_DIR | absolute path to the blast+ executable directory (bin)|
| MUSCLE_EXE | absolute path the the muscle executable file |
| FASTTREE_EXE | absolute path to the fasttree executable file |
| IQTREE_EXE | absolute path to the IQTree executable file |
| PHANTASM_DIR | absolute path to the phantasm directory |
| XENOGI_DIR | absolute path to the xenoGI directory |
|_______________________________________________________________________|
There are also optional values in param.py that can be modified in order to customize how PHANTASM runs. See the docker tutorial for more information.
To check that dependencies are properly installed, run the following command:
python3 <path to phantasm>/phantasm.py check
If no error occurs, then all dependencies are properly installed.
A detailed tutorial exists for the Docker image and the instructions are identical for using the conda installation. The only major difference between running phantasm natively and running phantasm in a Docker container is that the command phantasm should be replaced with python3 <path to phantasm>/phantasm.py. Alternatively, you can add the following line to your bash profile (.profile, .bashrc, etc.) which will allow your terminal to call phantasm with the command phantasm. Keep in mind that you will need to reload your terminal for the changes to take effect.
alias phantasm='python3 <absolute path to phantasm>/phantasm.py'
A help message can be obtained with the command python3 <path to phantasm>/phantasm.py help. Help messages for a given task can be obtained with the command python3 <path to phantasm>/phantasm.py <TASK> --help. The version of PHANTASM can be obtained with the command python3 <path to phantasm>/phantasm.py version. For help on analyzing the results, please see the detailed tutorial.
See section 1.2 for installation details.
- xenoGI v3.1.2
- scipy
- Bio
- textdistance
- numpy
- parasail
- rpy2
- pyani
- semver
- ape
- gplots
- dendextend
- DECIPHER