diff --git a/resources/singularity/htp/README.md b/resources/singularity/htp/README.md new file mode 100644 index 0000000000000000000000000000000000000000..0eb961330e82c997af688b818f9de06d54f3ef0a --- /dev/null +++ b/resources/singularity/htp/README.md @@ -0,0 +1,28 @@ +# 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 +``` + diff --git a/resources/singularity/htp/htp.def b/resources/singularity/htp/htp.def new file mode 100644 index 0000000000000000000000000000000000000000..9d3b57d3c1ca409d6ff4e2100719ff5322b2a735 --- /dev/null +++ b/resources/singularity/htp/htp.def @@ -0,0 +1,39 @@ +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