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Nikos Pappas
phap
Commits
04e6e104
Commit
04e6e104
authored
4 years ago
by
Nikos Pappas
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added host taxon predictor
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resources/singularity/htp/README.md
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resources/singularity/htp/README.md
resources/singularity/htp/htp.def
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# Host Taxon Predictor (HTP)
Available from
`library://papanikos_182/default/htp:1.0.2`
## Procedure
1.
Build the image with the definition file
```
$ sudo singularity build htp.sif htp.def
```
3.
[Optional] Sign the image
```
$ singularity sign htp.sif
```
4.
Push it on the cloud
```
$ singulairty push htp.sif library://papanikos_182/default/htp:1.0.2
```
## Usage
```
$ singularity run library://papanikos_182/default/htp:1.0.2 \
viruses_classifier -h
```
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resources/singularity/htp/htp.def
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Bootstrap: docker
From: continuumio/miniconda3
%labels
Author "Wojciech Gałan"
Maintainer papanikos_182
Version 1.0.2
Source https://github.com/wojciech-galan/viruses_classifier
Publication https://www.nature.com/articles/s41598-019-39847-2
%post
# Update OS
apt update && apt upgrade -y
# Install dependencies
conda config --add channels conda-forge
conda config --add channels default
conda config --add channels bioconda
conda config --add channels r
conda update -y conda
conda create -n htp python=2.7 scipy numpy scikit-learn pip
conda clean --all -y
echo ". /opt/conda/etc/profile.d/conda.sh" >> $SINGULARITY_ENVIRONMENT
echo "conda activate htp" >> $SINGULARITY_ENVIRONMENT
. /opt/conda/etc/profile.d/conda.sh
conda activate htp
pip install git+https://github.com/wojciech-galan/viruses_classifier.git
%help
A container for Host Taxon Predictor v0.1.2
[https://github.com/wojciech-galan/viruses_classifier].
To run htp help:
$ singularity exec library://papanikos_182/default/htp:1.0.2 viruses_classifier --help
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