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qiime2

qiime2 is a tool.

qiime2 can be found among the UPPMAX modules.

module spider qiime2
How does that look like?

You output will look similar to this:

[richel@rackham3 ~]$ module spider qiime2

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  qiime2:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
     Versions:
        qiime2/2018.11.0
        qiime2/2024.2

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  For detailed information about a specific "qiime2" package (including how to load the modules) use the module's full name.
  Note that names that have a trailing (E) are extensions provided by other modules.
  For example:

     $ module spider qiime2/2024.2
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

To find out how to load a specific version:

module spider qiime2/1.22.2
How does that look like?

Output will look similar to:

[richel@rackham3 ~]$ module spider qiime2/2024.2

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

qiime2: qiime2/2024.2
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

    You will need to load all module(s) on any one of the lines below before the "qiime2/2024.2" module is available to load.

      bioinfo-tools

    Help:
      qiime2 - use qiime2 

      Description

      Version 2024.2

      https://qiime2.org

      The version installed is 2024.2 amplicon, slightly modified from the publicly available docker image.


         qiime ...


      You may see a message like 

          Matplotlib created a temporary config/cache directory at /scratch/matplotlib-a10b2an0 because the default path (/home/qiime2/matplotlib) is not a writable directory...

      This is because qiime2 is running within an Apptainer container. This message can be ignored.

After reading that documentation, we know how to load it:

module load bioinfo-tools 
module load qiime2/2024.2
How does that look like?

Your output will look similar to this:

[richel@rackham3 ~]$ module load bioinfo-tools 
[richel@rackham3 ~]$ module load qiime2/2024.2
[richel@rackham3 ~]$

Singularity script

If you want to put qiime2 in a Singularity container, here is an example script:

BootStrap: library
From: centos:7

%runscript
  . /miniconda/etc/profile.d/conda.sh
  PATH=$PATH:/miniconda/bin
  conda activate qiime2-2019.7
  qiime "$@"

%post
  yum clean all
  yum -y update
  yum -y install wget python-devel
  cd /tmp
  wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
  bash ./Miniconda2-latest-Linux-x86_64.sh -b -p /miniconda
  /miniconda/bin/conda update -y conda
  wget https://data.qiime2.org/distro/core/qiime2-2019.7-py36-linux-conda.yml
  /miniconda/bin/conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-linux-conda.yml
  # OPTIONAL CLEANUP
  rm qiime2-2019.7-py36-linux-conda.yml
  /miniconda/bin/conda clean -a

See the documentation on Singularity how to do so.