graphlan
Link to section 'Introduction' of 'graphlan' Introduction
Graphlan is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees.
For more information, please check its website: https://biocontainers.pro/tools/graphlan and its home page: https://huttenhower.sph.harvard.edu/graphlan/.
Link to section 'Versions' of 'graphlan' Versions
- 1.1.3
Link to section 'Commands' of 'graphlan' Commands
- graphlan.py
- graphlan_annotate.py
Link to section 'Module' of 'graphlan' Module
You can load the modules by:
module load biocontainers
module load graphlan
Link to section 'Example job' of 'graphlan' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Graphlan on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=graphlan
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers graphlan
graphlan_annotate.py hmptree.xml hmptree.annot.xml --annot annot.txt
graphlan.py hmptree.annot.xml hmptree.png --dpi 150 --size 14