Qiime2 2019.7

Basic Information

Installation

Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6
  • Python \(\boldsymbol{\ge}\) 2.7

Build process

This entry described the installation process of Qiime2 in a Conda environment.

  1. Download the dependencies file for your Qiime version, in this example we download the 2019.7 version.

    wget https://data.qiime2.org/distro/core/qiime2-2019.7-py36-linux-conda.yml

  2. Create the environment.

    Note

    It’s highly recommend creating a new environment for each version of QIIME 2 release being installed.

    conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-linux-conda.yml

Testing

  1. Load the python module with conda.

    module load python

  2. Activate the conda environment source activate <environment-name>, this example we use the qiimw2-2019.7 environment.

    source activate qiime2-2019.7

  3. Run a simple command.

    qiime --help

Usage

This section describes the method to submit jobs with the resource manager SLURM.

slurm.sh
#!/bin/bash

#SBATCH --job-name=<job_name>       # Job name
#SBATCH --mail-type=ALL         # Mail notification
#SBATCH --mail-user=test@eafit.edu.co  # User Email
#SBATCH --output=%x.%j.out # Stdout (%j expands to jobId, %x expands to jobName)
#SBATCH --error=%x.%j.err  # Stderr (%j expands to jobId, %x expands to jobNam0e)
#SBATCH --ntasks=1                   # Number of tasks (processes)
#SBATCH --cpus-per-task=32           # Number of threads
#SBATCH --time=1-00:00               # Walltime
#SBATCH --partition=longjobs         # Partition


##### ENVIRONMENT CREATION #####
module load python
source activate qiime2-2019.7

##### JOB COMMANDS #### 
#3. Sequence quality control and feature table construction
qiime <plugin> <flags>

Note

For more information about plugins, read the qiime2 documentation

Authors