Qiime2 2018.4

Basic information

Tested on (Requirements)

  • Dependencies to run Qiime2:
    • Python >= 3.6.5 (Miniconda)

Installation

  1. Charge the environment and perform the following steps for installation:

    module load python/3.6.5_miniconda-4.5.1
cd /home/mgomezzul/apps/qiime2
wget https://data.qiime2.org/distro/core/qiime2-2018.4-py35-linux-conda.yml
conda env create -n qiime2-2018.4 --file qiime2-2018.4-py35-linux-conda.yml

Mode of Use

Load the necessary environment through the modules:

module load python/3.6.5_miniconda-4.5.1
source activate qiime2-2018.4

SLURM Template

#!/bin/sh

#SBATCH --partition=longjobs
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16
#SBATCH --time=10:00
#SBATCH --job-name=qiime2_test
#SBATCH -o result_%N_%j.out
#SBATCH -e result_%N_%j.err

# Don't share environment variables
export SBATCH_EXPORT=NONE
export OMP_NUM_THREADS=$SLURM_NTASKS

module load python/3.6.5_miniconda-4.5.1

source activate qiime2-2018.4

qiime tools import --type EMPPairedEndSequences \
    --input-path /home/mgomezzul/test/qiime2/source \
    --output-path /home/mgomezzul/test/qiime2/result.qza

Input files

  • Remember to create the source directory in the place where the slurm.sh file is located
  • Have the files (barcodes.fastq.gz, forward.fastq.gz, reverse.fastq.gz)

Authors

  • Mateo Gómez Zuluaga