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Commit 1ddbe8e6 authored by Nikos Pappas's avatar Nikos Pappas
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update vhulk def file

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Bootstrap: docker
bootstrap: docker
From: continuumio/miniconda3
%labels
Maintainer papanikos_182
Version 0.1
Source https://github.com/LaboratorioBioinformatica/vHULK
Preprint https://www.biorxiv.org/content/10.1101/2020.12.06.413476v1
%files
vhulk_explicit.txt /opt/vHULK/
vHULK /opt
vhulk_resources.tar.gz /opt/vHULK
Maintainer papanikos_182
Version 1.0.0
Source https://github.com/LaboratorioBioinformatica/vHULK
Preprint https://www.biorxiv.org/content/10.1101/2020.12.06.413476v1
%environment
export PATH=/opt/vHULK:$PATH
export PATH=/opt/vHULK:$PATH
%post
apt update && apt upgrade -y
conda update -y conda
conda create -n vhulk --file=/opt/vHULK/vhulk_explicit.txt
apt update && apt upgrade -y
conda update -y conda
# Grab source
git clone https://github.com/LaboratorioBioinformatica/vHULK.git /opt/vHULK
conda env create -n vhulk -f=/opt/vHULK/vhulk.yml
conda clean -ya
echo ". /opt/conda/etc/profile.d/conda.sh" >> $SINGULARITY_ENVIRONMENT
echo "conda activate vhulk" >> $SINGULARITY_ENVIRONMENT
tar -xvzf /opt/vHULK/vhulk_resources.tar.gz -C /opt/vHULK && rm /opt/vHULK/vhulk_resources.tar.gz
echo ". /opt/conda/etc/profile.d/conda.sh" >> $SINGULARITY_ENVIRONMENT
echo "conda activate vhulk" >> $SINGULARITY_ENVIRONMENT
. /opt/conda/etc/profile.d/conda.sh
conda activate vhulk
cd /opt/vHULK
# Grab models
python download_and_set_models.py
chmod -R g+Xr,o+Xr models/
%help
A container for vHULK v0.1 ( https://github.com/LaboratorioBioinformatica/vHULK ).
A container for vHULK v1.0.0 ( https://github.com/LaboratorioBioinformatica/vHULK ).
Required source scripts. models and data are stored in /opt/vHULK .
Required source scripts. models and data are stored in /opt/vHULK .
The main vHULK-v0.1.py has been modified with
- Portable shebang
- All hardcoded paths are now hardcoded for this container
To run the help menu for vHULK from this container execute
To run the help menu for vHULK from this container execute
$ singularity exec library://papanikos_182/vhulk:0.1 python vHULK-v0.1.py --help
$ singularity exec library://papanikos_182/vhulk:0.1 python vHULK-v0.1.py --help
vHULK takes an input directory with one or more fasta files that are assumed to
be bins. It makes predictions based on its models for all bins separately.
That is, if you have assembled contigs you need to split them into separate files
in a directory and provide that as input.
It outputs a dir named `results`, stored within the input dir (nobody knows why..).
Its major output is a `results.csv` file with host predictions for each genome.
The results dir also contains hmmscan results and prokka annotations for all input
genomes/bins.
To run an anlysis for all genomes stored in the /path/to/genomes, with 8 threads
To run an anlysis for all genomes stored in the /path/to/genomes, with 8 threads
$ singularity exec library://papanikos_182/default/vhulk:0.1 \
python vHULK_v0.1.py -i /path/to/genomes -t 8
$ singularity exec library://papanikos_182/default/vhulk:0.1 \
vHULK.py -i /path/to/genomes -o output_dir -t 8
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