QIIME/fr: Difference between revisions
(Created page with "QIIME") |
(Updating to match new version of source page) |
||
| Line 1: | Line 1: | ||
<languages /> | <languages /> | ||
'''QIIME''' ( | '''QIIME''' (pronounced ''chime'') stands for ''Quantitative Insights Into [https://en.wikipedia.org/wiki/Microbial_ecology Microbial Ecology]'', is an open-source [https://en.wikipedia.org/wiki/Bioinformatics bioinformatics] pipeline for performing [https://en.wikipedia.org/wiki/Microbiota microbiome] analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on [https://www.illumina.com/ Illumina] or other platforms to publication-quality graphics and statistics. This includes demultiplexing and quality filtering, [https://en.wikipedia.org/wiki/Operational_taxonomic_unit OTU] picking, taxonomic assignment, phylogenetic reconstruction, diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples. | ||
'''Note''': QIIME 2 has | '''Note''': QIIME 2 has replaced QIIME 1 as of January 1, 2018; version 1 is no longer supported. | ||
= | ==Installation == | ||
QIIME 2 can be installed in your home directory using conda. It is not possible to install this software using pip at this time. | |||
The installation procedure depends on whether or not you have a [https://www.anaconda.com/ conda] environment. | |||
===With conda environment=== | ===With a conda environment=== | ||
Although we '''do not recommend''' using conda environments in an HPC environment, we provide the option to do so at your own peril | Although we '''do not recommend''' using conda environments in an HPC environment, we provide the option to do so at your own peril. | ||
General installation instructions by the QIIME 2 developers are found [https://docs.qiime2.org/ here]. Instructions adapted for Compute Canada systems are given here for version 2019.7. If a new version of the <tt>.yml</tt> file is released (check the link), use the newer version by updating the instructions below. | |||
<pre> | <pre> | ||
eb Miniconda3-4.5.12.eb | eb Miniconda3-4.5.12.eb | ||
| Line 23: | Line 22: | ||
conda activate qiime2-2019.7 | conda activate qiime2-2019.7 | ||
</pre> | </pre> | ||
Remember to log out and back in after "conda init bash" step. | Remember to log out and log back in after the "conda init bash" step. | ||
To use | To run QIIME 2, use | ||
<pre> | <pre> | ||
module load miniconda3 | module load miniconda3 | ||
| Line 31: | Line 30: | ||
</pre> | </pre> | ||
===Without conda environment (preferred)=== | ===Without a conda environment (preferred)=== | ||
Since we know that conda environments can create more problems that | Since we know that conda environments can create more problems that they solve in HPC systems, we provide EasyBuild packages that can be used with the <tt>eb</tt> command. To install version 2019.7, use | ||
<pre> | <pre> | ||
eb --rebuild Miniconda3-4.7.10.eb QIIME2-2019.7.eb | eb --rebuild Miniconda3-4.7.10.eb QIIME2-2019.7.eb | ||
</pre> | </pre> | ||
This | This takes a while, but will provide you with the qiime/2019.7 module that you need to load before using QIIME 2. | ||
<pre> | <pre> | ||
module load qiime2/2019.7 | module load qiime2/2019.7 | ||
</pre> | </pre> | ||
= | =References = | ||
[http://qiime.org/ QIIME homepage]<br> | [http://qiime.org/ QIIME homepage]<br> | ||
[https://easybuild.readthedocs.io/en/latest/ | [https://easybuild.readthedocs.io/en/latest/ EasyBuild documentation]<br> | ||
[https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html Getting started with Conda]<br> | [https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html Getting started with Conda]<br> | ||
[[Category:Bioinformatics]] | [[Category:Bioinformatics]] | ||
[[Category:User Installed Software]] | [[Category:User Installed Software]] | ||
Revision as of 20:16, 6 February 2020
QIIME (pronounced chime) stands for Quantitative Insights Into Microbial Ecology, is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on Illumina or other platforms to publication-quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, phylogenetic reconstruction, diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.
Note: QIIME 2 has replaced QIIME 1 as of January 1, 2018; version 1 is no longer supported.
Installation
QIIME 2 can be installed in your home directory using conda. It is not possible to install this software using pip at this time.
The installation procedure depends on whether or not you have a conda environment.
With a conda environment
Although we do not recommend using conda environments in an HPC environment, we provide the option to do so at your own peril.
General installation instructions by the QIIME 2 developers are found here. Instructions adapted for Compute Canada systems are given here for version 2019.7. If a new version of the .yml file is released (check the link), use the newer version by updating the instructions below.
eb Miniconda3-4.5.12.eb module load miniconda3 conda update conda wget https://data.qiime2.org/distro/core/qiime2-2019.7-py36-linux-conda.yml conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-linux-conda.yml conda init bash conda activate qiime2-2019.7
Remember to log out and log back in after the "conda init bash" step.
To run QIIME 2, use
module load miniconda3 conda activate qiime2-2019.7
Without a conda environment (preferred)
Since we know that conda environments can create more problems that they solve in HPC systems, we provide EasyBuild packages that can be used with the eb command. To install version 2019.7, use
eb --rebuild Miniconda3-4.7.10.eb QIIME2-2019.7.eb
This takes a while, but will provide you with the qiime/2019.7 module that you need to load before using QIIME 2.
module load qiime2/2019.7
References
QIIME homepage
EasyBuild documentation
Getting started with Conda