Installation

MIMA Container image

All tools required by the MIMA pipeline are encapsulated into a Container image file with the mimaX_vX.X.X_yyyyddmm.sif naming scheme, where XXX denotes different versions.

The latest MIMA container version (mima4_v2.0.0) supports HUMAnN v3.8 and MetaPhlAn v4.1.0 tools and their reference database (older reference databases will not work).

Start an interactive PBS job

We assume you are on a HPC environment with a job scheduling system. Many HPC environments will not allow running containers from the login or head node. You need to start an interactive PBS job first.

  • In OpenPBS, specify the following to request an interactive job with 4 CPUs, 4GB ram for 6 hours
qsub -I -l select=1:ncpus=4:mem=4gb,walltime=6:00:00
  • Optional: if apptainer (or singularity) is installed via Modules on your host machine, then run the following
module load apptainer
apptainer --version

at the time of writing this tutorial we were using apptainer version 1.2.4-1el.8

Build a sandbox

As mentioned previously, to skip repeated unpacking the image when we deploy containers, we will build a sandbox container.

  • Build a sandbox called mima-pipeline
    • below shows command for the two MIMA versions
apptainer build --sandbox mima-pipeline mima4_v2.0.0_20240409.sif

INFO:    Starting build...
INFO:    Verifying bootstrap image mima4_v2.0.0_20240409.sif
INFO:    Creating sandbox directory...
INFO:    Build complete:
  • Create a SANDBOX environment variable to store the full directory path (saves typing a long paths!)
export SANDBOX=`pwd`/mima-pipeline

Confirm installation

  • Test SANDBOX environment variable is working
  • If this command is not working then check your SANDBOX environment variable using echo $SANDBOX which should output the path where you build the sandbox
apptainer run $SANDBOX

Below is the output, check the line active environment : mima is the same as below

----
source: /opt/miniconda/envs/mima/etc/conda/activate.d/activate-binutils_linux-64.sh:10:40: parameter expansion requires a literal
source: /opt/miniconda/envs/mima/etc/conda/activate.d/activate-gcc_linux-64.sh:10:40: parameter expansion requires a literal
source: /opt/miniconda/envs/mima/etc/conda/activate.d/activate-gfortran_linux-64.sh:10:40: parameter expansion requires a literal
source: /opt/miniconda/envs/mima/etc/conda/activate.d/activate-gxx_linux-64.sh:10:40: parameter expansion requires a literal
Auto-activate MIMA conda environment
source: /opt/miniconda/envs/mima/etc/conda/deactivate.d/deactivate-gxx_linux-64.sh:10:40: parameter expansion requires a literal
source: /opt/miniconda/envs/mima/etc/conda/deactivate.d/deactivate-gfortran_linux-64.sh:10:40: parameter expansion requires a literal
source: /opt/miniconda/envs/mima/etc/conda/deactivate.d/deactivate-gcc_linux-64.sh:10:40: parameter expansion requires a literal
source: /opt/miniconda/envs/mima/etc/conda/deactivate.d/deactivate-binutils_linux-64.sh:10:40: parameter expansion requires a literal
source: /opt/miniconda/envs/mima/etc/conda/activate.d/activate-binutils_linux-64.sh:10:40: parameter expansion requires a literal
source: /opt/miniconda/envs/mima/etc/conda/activate.d/activate-gcc_linux-64.sh:10:40: parameter expansion requires a literal
source: /opt/miniconda/envs/mima/etc/conda/activate.d/activate-gfortran_linux-64.sh:10:40: parameter expansion requires a literal
source: /opt/miniconda/envs/mima/etc/conda/activate.d/activate-gxx_linux-64.sh:10:40: parameter expansion requires a literal
----
This is the MIMA pipeline Container
v2.0.0 - build: 20240409

   active environment : mima
  active env location : /opt/miniconda/envs/mima
          shell level : 1
     user config file : /home/z3534482/.condarc
populated config files : /home/z3534482/.condarc
        conda version : 24.1.2
  conda-build version : not installed
       python version : 3.12.1.final.0
               solver : libmamba (default)
     virtual packages : __archspec=1=zen2
                        __conda=24.1.2=0
                        __glibc=2.35=0
                        __linux=4.18.0=0
                        __unix=0=0
     base environment : /opt/miniconda  (read only)
    conda av data dir : /opt/miniconda/etc/conda
conda av metadata url : None
         channel URLs : https://conda.anaconda.org/biobakery/linux-64
                        https://conda.anaconda.org/biobakery/noarch
                        https://conda.anaconda.org/conda-forge/linux-64
                        https://conda.anaconda.org/conda-forge/noarch
                        https://conda.anaconda.org/bioconda/linux-64
                        https://conda.anaconda.org/bioconda/noarch
                        https://repo.anaconda.com/pkgs/main/linux-64
                        https://repo.anaconda.com/pkgs/main/noarch
                        https://repo.anaconda.com/pkgs/r/linux-64
                        https://repo.anaconda.com/pkgs/r/noarch
                        https://conda.anaconda.org/default/linux-64
                        https://conda.anaconda.org/default/noarch
        package cache : /opt/miniconda/pkgs
                        /home/z3534482/.conda/pkgs
     envs directories : /home/z3534482/.conda/envs
                        /opt/miniconda/envs
             platform : linux-64
           user-agent : conda/24.1.2 requests/2.31.0 CPython/3.12.1 Linux/4.18.0-513.24.1.el8_9.x86_64 ubuntu/22.04.4 glibc/2.35 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.3
              UID:GID : 13534482:5000
           netrc file : None
         offline mode : False


Python 3.10.8
Rscript (R) version 4.2.1 (2022-06-23)
humann v3.8
MetaPhlAn version 4.1.0 (23 Aug 2023)
java -ea -Xmx97655m -Xms97655m -cp /opt/miniconda/envs/mima/opt/bbmap-39.01-1/current/ clump.Clumpify --version
BBMap version 39.01
For help, please run the shellscript with no parameters, or look in /docs/.
fastp 0.23.4
2.28-r1209
Kraken version 2.1.3
Copyright 2013-2023, Derrick Wood (dwood@cs.jhu.edu)

Next check you have all the required data-dependencies.


Last modified 25.09.2024