PhyloAcc

https://phyloacc.github.io
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PhyloAcc is a Bayesian program designed to detect shifts of DNA substitution rates in conserved...
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### Run Miniforge3 install script

Source: https://phyloacc.github.io/install.html

Run the downloaded Miniforge3 install script. Replace <filename> with the actual script name. Follow the prompts and restart your shell after installation.

```bash
bash <filename>.sh
```

--------------------------------

### Generate a config file with phyloacc_workflows init

Source: https://phyloacc.github.io/workflow.html

Quick start method to create a starting config file with required fields left blank. Run this command in your terminal.

```bash
./phyloacc_workflows init -o my-config.yaml
```

--------------------------------

### Install PhyloAcc with conda

Source: https://phyloacc.github.io/index.html

Alternative installation using conda instead of mamba. Mamba is recommended for faster installation.

```bash
conda install phyloacc
```

--------------------------------

### Verify PhyloAcc installation with version and dependency checks

Source: https://phyloacc.github.io/install.html

Run 'phyloacc.py --version' to print version info and 'phyloacc.py --depcheck' to ensure C++ binaries are installed. Errors indicate installation issues.

```bash
phyloacc.py --version
```

```bash
phyloacc.py --depcheck
```

--------------------------------

### Run phyloacc.py with command-line options

Source: https://phyloacc.github.io/readme.html

Example command-line invocation of phyloacc.py with specific options: alignment file, BED file, mod file, and target branches. This is the command-line equivalent of the config file example.

```bash
phyloacc.py -a alignment.fa -b loci.bed -m model.mod -t "species1;species2;species3"
```

--------------------------------

### Install PhyloAcc from Bioconda

Source: https://phyloacc.github.io/install.html

Installs PhyloAcc from Bioconda using mamba. Follow the prompts and wait for dependencies to install.

```bash
mamba install phyloacc
```

--------------------------------

### Copy the full config template

Source: https://phyloacc.github.io/workflow.html

Alternative method to get a fully-commented config template by copying it from the repository's internal path.

```bash
cp config-template.yaml my-config.yaml
```

--------------------------------

### Make phyloacc_workflows executable

Source: https://phyloacc.github.io/workflow.html

If you get 'Permission denied' when running ./phyloacc_workflows, make the script executable with this command and try again.

```bash
chmod +x phyloacc_workflows
```

--------------------------------

### Set up conda environment with phyloacc_workflows setup

Source: https://phyloacc.github.io/workflow.html

Creates a dedicated conda environment named 'phyloacc-workflows' with all required dependencies. Re-running this command after changes to envs/environment.yml updates the existing environment.

```bash
./phyloacc_workflows setup
```

--------------------------------

### Specify phyloacc.py options in a YAML config file

Source: https://phyloacc.github.io/readme.html

Example YAML configuration file (phyloacc-cfg.yaml) that specifies the same options as the command-line example: alignment, bed, mod, and targets. This file is used with the --config option.

```yaml
alignment: alignment.fa
bed: loci.bed
mod: model.mod
targets: "species1;species2;species3"
```

--------------------------------

### Run phyloacc.py with a config file

Source: https://phyloacc.github.io/readme.html

Command to run phyloacc.py using a YAML config file with the --config option. This is equivalent to the command-line example.

```bash
phyloacc.py --config phyloacc-cfg.yaml
```

--------------------------------

### Create PhyloAcc conda environment

Source: https://phyloacc.github.io/install.html

Create a conda environment named phyloacc-env for installing and running PhyloAcc.

```bash
mamba create -n phyloacc-env
```

--------------------------------

### Initialize mamba and provide full path if needed

Source: https://phyloacc.github.io/install.html

If conda or mamba is not initialized, run 'mamba init' and restart the shell. If that fails, provide the full path to the mamba executable, e.g., '/where/you/installed/miniforge3/bin/mamba'.

```bash
mamba init
```

```bash
/where/you/installed/miniforge3/bin/mamba
```

--------------------------------

### Check if mamba/conda is installed

Source: https://phyloacc.github.io/install.html

Run this command to check if mamba and conda are already installed. If the output shows 'mamba X.X.X conda X.X.X', they are installed and you can skip to step 3.

```bash
mamba --version
```

--------------------------------

### Execute workflow: ./phyloacc_workflows run --configfile my-config.yaml -j 20 -e slurm

Source: https://phyloacc.github.io/workflow.html

Run the workflow after the dry run looks correct. Drop --dryrun to actually execute. Runtime can range from minutes to many hours depending on alignment size and number of chromosomes/scaffolds. Snakemake prints progress, and each rule writes its own log under <output_dir>/logs/<rule name>/.

```bash
./phyloacc_workflows run --configfile my-config.yaml -j 20 -e slurm
```

--------------------------------

### Set up batches for species tree model with phyloacc.py

Source: https://phyloacc.github.io/readme.html

Command-line invocation of phyloacc.py to set up batches of loci for the species tree model. Requires a directory of FASTA alignments, a mod file from phyloFit, and an output directory. Options include target branches, number of jobs, processes per job, batch size, and SLURM partitions.

```bash
phyloacc.py \
    -d [directory containing multiple FASTA formatted nucleotide alignments] \
    -m [mod file from phyloFit with input tree and neutral rate matrix] \
    -o [desired output directory] \
    -t "[semi-colon separated list of target branches in the species tree]" \
    -j [number of jobs/batches to split the input alignments into] \
    -p [processes to use per job/batch of alignments] \
    -batch [number of alignments per job/batch] \
    -part "[comma separated list of SLURM partitions to submit batches to as jobs]"
```

--------------------------------

### Activate the PhyloAcc conda environment

Source: https://phyloacc.github.io/install.html

Activates the 'phyloacc-env' environment using mamba. Required before installing or running software in the environment.

```bash
mamba activate phyloacc-env
```

--------------------------------

### Gather outputs with phyloacc_post.py

Source: https://phyloacc.github.io/readme.html

Command to run phyloacc_post.py, specifying the output directory that was used when running phyloacc.py.

```bash
phyloacc_post.py \
    -i [path output directory specified when running phyloacc.py]
```

--------------------------------

### Set up batches for gene tree model with phyloacc.py

Source: https://phyloacc.github.io/readme.html

Command-line invocation of phyloacc.py to set up batches of loci for the gene tree model. Requires a directory of FASTA alignments, a mod file, and a Newick species tree with branch lengths in coalescent units. Uses the -r gt option.

```bash
phyloacc.py \
    -d [directory containing multiple FASTA formatted nucleotide alignments] \
    -m [mod file from phyloFit with input tree and neutral rate matrix] \
    -r gt \
    -l [file with Newick formatted species tree with branch lengths in coalescent units] \
    -o [desired output directory] \
    -t "[semi-colon separated list of target branches in the species tree]" \
    -j [number of jobs/batches to split the input alignments into] \
    -p [processes to use per job/batch of alignments] \
    -batch [number of alignments per job/batch] \
    -part "[comma separated list of SLURM partitions to submit batches to as jobs]"
```

--------------------------------

### Download repository archive with wget

Source: https://phyloacc.github.io/workflow.html

Alternative to git: download the main branch archive directly from GitHub using wget. Extract the archive and work in the resulting directory.

```bash
wget https://github.com/phyloacc/phyloacc-workflows/archive/main.zip
```

--------------------------------

### Update conda to fix environment solving issues

Source: https://phyloacc.github.io/install.html

Run this command to update conda to the latest version, which may resolve issues where 'mamba install phyloacc' fails or hangs due to dependency solving problems.

```bash
conda update -n base -c defaults conda
```

--------------------------------

### Set up batches with adaptive model using sCF cutoffs

Source: https://phyloacc.github.io/readme.html

Command-line invocation of phyloacc.py to set up batches of loci with the model determined by sCF cutoffs. Requires a directory of FASTA alignments, a mod file, and a Newick species tree with branch lengths in coalescent units. Uses the -r adaptive option.

```bash
phyloacc.py \
    -d [directory containing multiple FASTA formatted nucleotide alignments] \
    -m [mod file from phyloFit with input tree and neutral rate matrix] \
    -r adaptive \
    -l [file with Newick formatted species tree with branch lengths in coalescent units] \
    -o [desired output directory] \
    -t "[semi-colon separated list of target branches in the species tree]" \
    -j [number of jobs/batches to split the input alignments into] \
    -p [processes to use per job/batch of alignments] \
    -batch [number of alignments per job/batch] \
    -part "[comma separated list of SLURM partitions to submit batches to as jobs]"
```

--------------------------------

### Check conda environment readiness

Source: https://phyloacc.github.io/workflow.html

Confirms that the phyloacc-workflows conda environment is ready. Use this at any time to verify the environment is correctly set up.

```bash
./phyloacc_workflows check
```

--------------------------------

### Dry run command: ./phyloacc_workflows run --configfile my-config.yaml -j 20 -e slurm --dryrun

Source: https://phyloacc.github.io/workflow.html

Run a dry run to validate the config file and see what jobs Snakemake plans to run before submitting anything. -j 20 sets the maximum number of concurrent jobs, and -e slurm submits jobs to a SLURM cluster using per-rule resources from rule_resources in the config. If testing on a single machine, drop -e slurm to run locally using up to -j CPU cores. Do not run without an executor on a login node.

```bash
./phyloacc_workflows run --configfile my-config.yaml -j 20 -e slurm --dryrun
```

--------------------------------

### Verify .condarc file with cat command

Source: https://phyloacc.github.io/install.html

Run this command to confirm your .condarc file is set up correctly. The output should match the .condarc contents shown above.

```bash
cat ~/.condarc
```

--------------------------------

### Clone the repository with git

Source: https://phyloacc.github.io/workflow.html

Use this command to clone the phyloacc-workflows repository from GitHub. After cloning, work in the phyloacc-workflows directory or provide full paths to workflow files.

```bash
git clone https://github.com/phyloacc/phyloacc-workflows.git
```
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