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{bio}[system/system] nullarbor v2.0.20191013 #9778

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{bio}[system/system] nullarbor v2.0.20191013 #9778

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45 changes: 45 additions & 0 deletions easybuild/easyconfigs/n/nullarbor/nullarbor-2.0.20191013.eb
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##
# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
# Homepage: https://staff.flinders.edu.au/research/deep-thought
#
# Authors:: Robert Qiao <rob.qiao@flinders.edu.au>
# License:: GPLv2.0
#
# Notes:: This is a conda version installation
##

easyblock = 'Conda'

name = 'nullarbor'
version = '2.0.20191013'

homepage = 'https://github.com/tseemann/nullarbor'
description = """
Pipeline to generate complete public health microbiology reports from sequenced isolates
"""

toolchain = SYSTEM

channels = ['conda-forge', 'bioconda']

requirements = '%(name)s=%(version)s python=3.6'

dependencies = [
('Miniconda3', '4.7.10', '', True)
]

sanity_check_commands = [('nullarbor.pl', '-h')]
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there is nullarbor.pl --check, but if fails with missing databases, should those also be installed?

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@manifestoso manifestoso Mar 13, 2020 •
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@migueldiascosta Thx for pointing --check option. I think it's a duplicate feature as sanity_check checks dir /perl5 which contains perl modules, files checks all binaries.
You probably are right, a more explicit option can be invoked to check each required perl modules.

A complete nullarbor has two parts framework and dataset, this easyconfig only cater framework part. Given the reference database is of a reasonable size 24G altogether and different research may use different reference databases, I would prefer to leave this part to the individual institution. I can append a few lines of instructions at the end, see what you @migueldiascosta think.


sanity_check_paths = {
'files': [
'bin/nullarbor.pl',
'bin/nullarbor-json.pl',
'bin/nullarbor-report.pl'],
'dirs': [
'bin',
'perl5',
'binaries',
'plugins'],
}

moduleclass = 'bio'