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mkweskin/viridal_def_file

Created December 17, 2021 15:22
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VirIdAl singularity def file
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viridal_def_file
Bootstrap: docker
From: continuumio/miniconda3
%post
/opt/conda/bin/conda config --add channels defaults
/opt/conda/bin/conda config --add channels bioconda
/opt/conda/bin/conda config --add channels conda-forge
/opt/conda/bin/conda config --add channels omnia
/opt/conda/bin/conda config --add channels plotly
/opt/conda/bin/conda install pandas samtools bedtools fastq_utils bowtie2 vsearch seqkit openmp diamond fastp termcolor plotly blast=2.11.0
/usr/bin/git clone https://github.com/budkina/VirIdAl
mv /VirIdAl/* /
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For https://github.com/budkina/VirIdAl
Run like this: singularity run --no-home --bind /path/to/database/directory:/database library://kweskinm/default/viridal:latest python download_databases.py --num_threads 4

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