mothulity

Simple tool to facilitate work with mothur. It can download a proper database, run SOP provided with just fastq files directory, draw few figures and wrap it all into fancy html. Handles slurm and sends e-mail notifications when the job is done (using headnode_notifier).

Contribution guidelines

Your are more than welcomed to contribute by:

Creating issue - see issue template:
- if you want to report a bug.
- if you want to propose an update.
- if you have a brilliant idea for a brand new feature
Create pull request - see pull request template:
- if you want to help with your own coding skills.

Installation

Install Anaconda.
git clone https://github.com/dizak/mothulity.
bash INSTALL.sh

Update

bash UPDATE.sh

Usage

Databases

mothulity needs databases to operate. Databases can be placed anywhere. The paths should be specified by the CLI or in the config file. CLI overrides the config file settings. User is asked whether download and set default paths during installation.

Databases download is handled by mothulity_dbaser.py /path/where/database/should/be/downloaded --type-of-database, eg mothulity_dbaser.py /home/user/mothulity/dbs --silva-119.
Databases default path set-up is handled by mothulity.py --set-align-database-path /path/to/database --set-taxonomy-database-path.

Basic usage

mothulity.py /path/to/fastq/files -r sh

Above command will run MiSeq SOP, draw plots, render html output and zip everything. Omit -r if you do not want the produced bash script to be executed. The -r option accepts any shell of choice. On a regular Linux machine it will be probably -r sh. On, let's say SLURM Queueing System: -r -sbatch. On TORQUE: -r qsub. Mothulity does not really care, it is the matter of the user's system.

You can send results in the email notification with:

mothulity.py /path/to/fastq/files -r sh --notify-email your.email@your.domain

As --notify-email depends on headnode_notifier, please check its repo for configuration instructions.

Example data

Presumably, it is a good idea to test mothulity with MiSeq SOP delivered by creators of mothur.

Requirements for manual installation

Anaconda users: install dependencies with
```
conda env create --file /path/to/mothulity.yaml
```
or if you have access restrictions (eg. anaconda is installed system-wide)
```
conda env create --file /path/to/mothulity.yaml -p /your/path/to/env/
```
and that's all.
non-conda users: beside installing packages listed in mothulity.yaml, you need:

Setnea/mothulity