motroy/singularity-scagaire:latest
$ singularity pull shub://motroy/singularity-scagaire:latest
Singularity Recipe
Bootstrap: docker
From: frolvlad/alpine-miniconda3:latest
%environment
export LC_ALL=C
export CONDARC=/.condarc
export PATH="/opt/conda/bin:/Software/scagaire/:/Software/scagaire/scagaire/:/Software/scagaire/scagaire/data/:$PATH"
export MPLBACKEND=TKAgg
%post
apk update && apk add git curl-dev wget less openssh-server parallel coreutils bash libx11 #py3-pip libcurl gcc musl-dev
/opt/conda/bin/conda config --file /.condarc --add channels defaults && /opt/conda/bin/conda config --file /.condarc --add channels conda-forge && /opt/conda/bin/conda config --file /.condarc --add channels bioconda
/opt/conda/bin/conda update -n base -c defaults conda
/opt/conda/bin/conda install -c conda-forge mamba
export PATH="/opt/conda/bin:$PATH"
mamba install -y -c bioconda mash abricate ncbi-genome-download
export MPLBACKEND=TKAgg
mkdir /Software && cd /Software
git clone https://github.com/quadram-institute-bioscience/scagaire.git
cd scagaire
python setup.py install
export PATH="/Software/scagaire/:/Software/scagaire/scagaire/:/Software/scagaire/scagaire/data/:$PATH"
Collection
- Name: motroy/singularity-scagaire
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/motroy-singularity-scagaire-latest |
collection name | motroy/singularity-scagaire |
branch | master |
tag | latest |
commit | c790e82f308d8b98c8f2bb5999d123203d1799ba |
version (container hash) | 4c6b78eacc78b0ee05a9653ef8d5e03e |
build date | 2020-08-17T10:39:56.997Z |
size (MB) | 1873.0 |
size (bytes) | 825761823 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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