# Contribution from the Crick HPC team
# uploaded by J. Sassmannshausen
#
# Updated to version 0.6.2: Pavel Grochal (INUITS)
# Updated to version 0.6.5: Alex Domingo (VUB)
#
# IT4Innovations JK 2021
# easyconfig taken from
# https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb
#

easyblock = 'Tarball'

name = 'Trim_Galore'
version = '0.6.6'
versionsuffix = '-Python-%(pyver)s'

homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/'
description = """Trim Galore is a wrapper around Cutadapt and FastQC to
consistently apply adapter and quality trimming to FastQ files, with extra
functionality for RRBS data."""

toolchain = {'name': 'GCC', 'version': '10.2.0'}

source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/']
sources = ['%(version)s.tar.gz']
checksums = ['b8db8ffd131d9d9e7c8532a5a1f1caee656c0c58d3eafd460fee3c39b9fcab5e']

builddependencies = [('binutils', '2.35')]

dependencies = [
    ('Python', '2.7.18'),
    ('Java', '11', '', True),
    ('pigz', '2.6'),
    ('Perl', '5.32.0'),
    ('FastQC', '0.11.9', '-Java-%(javaver)s', True),
    ('cutadapt', '1.18', versionsuffix),
]

postinstallcmds = [
    "chmod +x %(installdir)s/%(namelower)s",
    "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s",
    "mkdir %(installdir)s/bin && mv %(installdir)s/%(namelower)s %(installdir)s/bin/%(namelower)s",
]

sanity_check_paths = {
    'files': ["bin/trim_galore"],
    'dirs': [],
}

sanity_check_commands = [
    "trim_galore --help"
]

moduleclass = 'bio'