Filogenics environment with Anaconda 2024
Filogenics environment with Anaconda 2024 is a custom Anaconda 2024 environment with ready to use tools for Filogenic research. The apps included are:
- FastQC
- fastp
- AdapterRemoval
- bwa
- Samtools
- mapDamage
- RAxML
- IQTREE2
- MrBayes
- Beast2
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-filogenics.sh
#!/bin/bssh
#SBATCH -J test-filogenics
#SBATCH --output=test-filogenics-%j.out
#SBATCH --error=test-filogenics-%j.err
#SBATCH -p thin
#SBATCH -N 1
export CRYPTOGRAPHY_OPENSSL_NO_LEGACY=1
module load filogenics/2024
# FastQC#
fastqc --help
# fastp
fastp --help
# AdapterRemoval
AdapterRemoval --help
# bwa
bwa
# Samtools
samtools --help
# mapDamage
mapDamage --help
# RAxML
raxmlHPC -h
# IQTREE2
iqtree2 --help
# MrBayes
mb -h
# Beast2
beast -version
Submit with :
sbatch --account=your_project_ID test-filogenics.sh
More info :