QIIME2-Teaching: Difference between revisions
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=== Version === | === Version === | ||
2018. | 2018.6 | ||
=== Author / Distributor === | === Author / Distributor === | ||
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=== Running Program === | === Running Program === | ||
The last version of this application is at /usr/local/apps/eb/QIIME2/2018. | The last version of this application is at /usr/local/apps/eb/QIIME2/2018.6 | ||
To use this version, please load the module with | To use this version, please load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml QIIME2/2018. | ml QIIME2/2018.6 | ||
</pre> | </pre> | ||
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cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml QIIME2/2018. | ml QIIME2/2018.6<br> | ||
qiime <u>[options]</u><br> | qiime <u>[options]</u><br> | ||
</div> | </div> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml QIIME2/2018. | ml QIIME2/2018.6 | ||
qiime | qiime | ||
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. | QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. |
Revision as of 15:46, 15 August 2018
Category
Bioinformatics
Program On
Teaching
Version
2018.6
Author / Distributor
Description
"QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data." More details are at QIIME2
Running Program
The last version of this application is at /usr/local/apps/eb/QIIME2/2018.6
To use this version, please load the module with
ml QIIME2/2018.6
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_QIIME2
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=QIIME2.%j.out
#SBATCH --error=QIIME2.%j.err
cd $SLURM_SUBMIT_DIR
ml QIIME2/2018.6
qiime [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml QIIME2/2018.6 qiime QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. Usage: qiime [OPTIONS] COMMAND [ARGS]... QIIME 2 command-line interface (q2cli) -------------------------------------- To get help with QIIME 2, visit https://qiime2.org. To enable tab completion in Bash, run the following command or add it to your .bashrc/.bash_profile: source tab-qiime To enable tab completion in ZSH, run the following commands or add them to your .zshrc: autoload bashcompinit && bashcompinit && source tab-qiime Options: --version Show the version and exit. --help Show this message and exit. Commands: info Display information about current deployment. tools Tools for working with QIIME 2 files. dev Utilities for developers and advanced users. alignment Plugin for generating and manipulating alignments. composition Plugin for compositional data analysis. cutadapt Plugin for removing adapter sequences, primers, and other unwanted sequence from sequence data. dada2 Plugin for sequence quality control with DADA2. deblur Plugin for sequence quality control with Deblur. demux Plugin for demultiplexing & viewing sequence quality. diversity Plugin for exploring community diversity. emperor Plugin for ordination plotting with Emperor. feature-classifier Plugin for taxonomic classification. feature-table Plugin for working with sample by feature tables. fragment-insertion Plugin for extending phylogenies. gneiss Plugin for building compositional models. longitudinal Plugin for paired sample and time series analyses. metadata Plugin for working with Metadata. phylogeny Plugin for generating and manipulating phylogenies. quality-control Plugin for quality control of feature and sequence data. quality-filter Plugin for PHRED-based filtering and trimming. sample-classifier Plugin for machine learning prediction of sample metadata. taxa Plugin for working with feature taxonomy annotations. vsearch Plugin for clustering and dereplicating with vsearch.
Installation
Source code is obtained from QIIME2
System
64-bit Linux