SOFT : VARUS
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Site du soft: https://github.com/Gaius-Augustus/VARUS
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LICENSE:
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GPLv3

See software documentation for more informations.

Location: /usr/local/bioinfo/src/VARUS
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Load binaries and environment:
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-> Version a77e689

#Need samtools, bamtools, fastq-dump, Star or Hitsat2
module load bioinfo/samtools-1.16.1 bioinfo/bamtools-2.5.0 bioinfo/sratoolkit.3.0.0 bioinfo/STAR-2.7.5a bioinfo/hisat2-2.1.0

module load bioinfo/VARUS-a77e689

By default the NCBI tool fastq-dump creates temporary files under ~/ncbi whose allocated space is very limited.
A simple solution consist in create (or move if it already exist) .ncbi directory in your work space and making a symbolic link to this
directory in your home

mkdir ~/work/.ncbi (or mv ~/.ncbi ~/work/)
ln -s ~/work/.ncbi  ~/.ncbi



Example directory for use on cluster:
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/usr/local/bioinfo/src/VARUS/example_on_cluster

To submit: sbatch test_VARUS-a77e689.sh

See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.