Biogenomics environment with Anaconda 2024
Biogenomics environment with Anaconda 2024 is a custom Anaconda 2024 environment with ready to use tools for Biogenomic research. The apps included are:
- FastQC
- MultiQC
- Bowtie2
- Bismark
- Trim-galore
- Bedtools
- Samtools
WARNING: If you do not know how to create your own anaconda environment in agustina cluster, please read the instruction below, otherwise send and email with your request to agustina@bifi.es for further assistance.
IMPORTANT: If you want to update or install new programs on this conda environment please contact support at agustina@bifi.es for further assistance, pointing out the programs to install or update with the version needed.
Usage
Example script : test-biogenomics.sh
#!/bin/bash
#SBATCH --job-name=test-biogenomics
#SBATCH --output=test-biogenomics-%j.msg
#SBATCH --error=test-biogenomics-%j.err
#SBATCH -p thin
#SBATCH -N 1
export CRYPTOGRAPHY_OPENSSL_NO_LEGACY=1
module load genomics/2024
echo "FASTQC"
fastqc --help
echo "MULTIQC"
multiqc --help
echo "BOWTIE2"
bowtie2 --help
echo "BISMARK"
bismark --help
echo "TRIM-GALORE"
trim-galore --help
echo "BEDTOOLS"
bedtools --help
echo "SAMTOOLS"
samtools --help
echo "DONE!!!!"
Submit with :
sbatch --account=your_project_ID test-biogenomics.sh
More info :