Skip to content
GitLab
Explore
Sign in
Register
Primary navigation
Search or go to…
Project
P
phap
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Package Registry
Model registry
Operate
Environments
Terraform modules
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
Nikos Pappas
phap
Commits
1ddbe8e6
Commit
1ddbe8e6
authored
4 years ago
by
Nikos Pappas
Browse files
Options
Downloads
Patches
Plain Diff
update vhulk def file
parent
dcba01a4
No related branches found
No related tags found
No related merge requests found
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
resources/singularity/vhulk/vhulk.def
+32
-38
32 additions, 38 deletions
resources/singularity/vhulk/vhulk.def
with
32 additions
and
38 deletions
resources/singularity/vhulk/vhulk.def
+
32
−
38
View file @
1ddbe8e6
B
ootstrap: docker
b
ootstrap: 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 v
1.
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
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment