phylobook_pipeline

A program pipeline to run through multiple programs from sequence alignment fasta file to the resuts ready to publish on phylobook server

Usage

In a working directory that contains sequence alignment fasta files, run

python3 WherePhylobookPipelineInstalled/script/phylobook.py -d WorkingDirectoryPath(default: .) -t SequenceType(nt or aa) -p NumberOfProcessors(default: 1)

• you have to provide the value of SequencType ('nt' for nuclotide sequences, 'aa' for amino acid sequences)
• the default value of numberOfProcessors is 1. You can run multiprocessors by providing the value > 1 based on your computer settings
• it will output enhanced ML tree and highlighter plot for each input sequence alignment fasta file(.fasta), ready for display and manipulate on phylobook server

Installation and Configuration

The pipeline consists of three programming components (run_phyml_batch, figtree-enhanced-command-line and [highlighter(https://github.com/MullinsLab/highlighter)). In order to process the pipeline successfully, you need to meet the requirements of the programming components

If you are wanting to run the pipeline in a Docker contianer, see the Docker section of this document.

1. Clone this repository in your designated directory

git clone https://github.com/MullinsLab/phylobook_pipeline.git

• it will create a directory called "phylobook_pipeline" in your designated directory (i.e. WherePhylobookPipelineInstalled)

2. Requirements for run_phyml_batch

a. Download PhyML in the directory "phylobook_pipeline"

cd phylobook_pipeline
git clone --branch v3.3.20220408 https://github.com/stephaneguindon/phyml.git

• the current release is v3.3.20220408
• it will create a subdirectory called "phyml"

b. Update files in order to output pairwise distances after running phyml

cd phyml/src
python WherePhylobookPipelineInstalled/script/updatefiles.py
cd ..

c. In the directory of phyml/, install phyml following the instructions on PhyML GitHub

3. Requirements for figtree-enhanced-command-line

• This source is an extension of Adam Rambaut's FigTree. The original source can be found here: https://github.com/rambaut/figtree/releases
• Build Requirements (for further modifying the source code): java 8
• Execution: A current version of figtree.jar can be found in WherePhylobookPipelineInstalled/figtree/figtree.jar

4. Requirements for highlighter_bot

In a virtual Python 3 environment:

pip3 install -r requirements.txt

 

Docker

phylobook_pipeline includes a Dockerfile and a docker-compose.yml file to allow it to run in a Docker container. Please follow these installation steps

1. Ensure you have Docker installed on your system

See https://www.docker.com/

2. Clone this repository in your designated directory

git clone https://github.com/MullinsLab/phylobook_pipeline.git

it will create a directory called "phylobook_pipeline" in your designated directory (i.e. WherePhylobookPipelineInstalled)

3. If you are running the container on a Linux computer

If you are running phylobook_pipeline on a Linux computer the files created by the pipeline will not have the correct user ownership. In order to get around this, edit the docker-compose.yml file to have your userid and groupid.

You can find these using the id command on the command line.

Edit line 12 in docker-compose.yml, deleting the # sign, and replacing the userid:groupid parts of the line.

    # user: userid:groupid

will be changed to look similar to:

    user: 1001:1001

4. Build and run the container

cd phylobook_pipeline
docker compose up -d --build

This will likely take more than a full minute, depending on the speed of your computer.

5. Start a command line inside the docker container

docker exec -it phylobook_pipeline bash

This will put you into a Linux command line where you can operate the pipeline.

You can exit using ^d (control key + d).

6. Getting data "into" the Docker container.

Under the default setup, the only portion of the host computer's file system that is visible within the Docker container is the phylobook_pipeline directory (and subfolders therein). Anything that gets created inside the docker's phylobook_pipeline directory will show up in the host machine. Thus the easiest way to make data available to the Phylobook Pipeline in the Docker container is to create a subdirectory under the phylobook_pipeline and move data there on the host machine. In order to make this directory writeable by the pipeline, use the Unix commands chown and chgrpto change the user and group of the directory to the user and group id's chosen above in step 3.