Created
December 17, 2021 15:22
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VirIdAl singularity def file
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| 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