Bioconda

General

• Home page: https://bioconda.github.io/index.html

• List of available packages: https://bioconda.github.io/conda-package_index.html

Bioconda on ARC

Available modules

To activate

$ module avail bioconda
-------------------- /global/software/Modules/4.6.0/modulefiles -----------------
bioconda/2024-10  

• BioConda/2024-10 is based on the bioconda and conda-forge channels.

It does not depend nor use the Anaconda base and anaconda channels to avoid any licensing complications.

It was installed in October 2024 and includes a large number of more popular BioConda packages.

You can load the module

$ module load bioconda/2024-10

### !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ###
This is a stub module. It does not activate the central BioConda install.
If you want to activate BioConda/2024-10 please use the following command in your job script:

source /global/software/bioconda/init-2024-10

Module activation does not work propely for this BioConda due to technical limitaions.
This may change in the future.
### !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ###

Loading bioconda/2024-10
  ERROR: Module evaluation aborted

The message indicate that the module cannot activate BioConda correctly, so you have to use the command

source /global/software/bioconda/init-2024-10

instead.

Once you have BioConda activated you can check the software

$ samtools --version
samtools 1.21
Using htslib 1.21
Copyright (C) 2024 Genome Research Ltd.

$ salmon --version
version : 0.8.1

$ kraken --version
Kraken version 1.1.1
Copyright 2013-2019, Derrick Wood, Jennifer Lu (jlu26@jhmi.edu)

Get the full list of installed packages:

$ conda list
....

or search for a specific package:

$ conda list STAR
# packages in environment at /global/software/bioconda/2024-10/envs/bioconda:
#
# Name                    Version                   Build  Channel
star                      2.7.11a              h0033a41_0    bioconda
star-fusion               1.7.0                         1    bioconda
staramr                   0.10.0             pyhdfd78af_0    bioconda
starcode                  1.4                  h031d066_5    bioconda
starfish                  0.2.2              pyhdfd78af_0    bioconda

Installing your own personal BioConda

If the preinstalled versions provided by the modules do not work for you, you can

• Install your own Conda, following these instructions.

• Create a new BioConda environment:

conda create -n bioconda

• Activate the environment:

conda activate bioconda

• Install the required packages

conda install -c bioconda samtools star salmon kraken

Using Conda in your job scripts

Centrally Installed BioConda

If you want to use the preinstalled BioConda environment: preinstalled-bioconda-job.slurm:

#! /bin/bash
# ====================================
#SBATCH --job-name=conda-test
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=4GB
#SBATCH --time=0-01:00:00
# ====================================
# Activate BioConda.
source /global/software/bioconda/init-2024-10

# Use the software here.
....
....

Personal Conda

If you are going to be using your own personal BioConda install: personal-conda-job.slurm:

#! /bin/bash
# ====================================
#SBATCH --job-name=conda-test
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=4GB
#SBATCH --time=0-01:00:00
# ====================================
# Activate Conda and then the environment.
source ~/software/init-conda
conda activate bioconda

# Use the software here.
....
....

Links

ARC Software pages