# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez
# sciCORE - University of Basel
# SIB Swiss Institute of Bioinformatics

easyblock = 'Tarball'

name = 'PRINSEQ'
version = '0.20.4'

homepage = 'http://prinseq.sourceforge.net'
description = """A bioinformatics tool to PRe-process and show INformation of SEQuence data."""

toolchain = {'name': 'goolf', 'version': '1.4.10'}

source_urls = ['http://sourceforge.net/projects/prinseq/files/standalone/']
sources = ['%(namelower)s-lite-%(version)s.tar.gz']

local_perl = 'Perl'
local_perlver = '5.16.3'
versionsuffix = '-%s-%s' % (local_perl, local_perlver)

dependencies = [
    (local_perl, local_perlver),
]

# these are the local_perl libraries dependencies
exts_defaultclass = 'PerlModule'
exts_filter = ("perldoc -lm %(ext_name)s ", "")

exts_list = [
    ('ExtUtils::Depends', '0.405', {
        'source_tmpl': 'ExtUtils-Depends-0.405.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'],
    }),
    ('ExtUtils::PkgConfig', '1.15', {
        'source_tmpl': 'ExtUtils-PkgConfig-1.15.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'],
    }),
    ('Getopt::Long', '2.48', {
        'source_tmpl': 'Getopt-Long-2.48.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV/'],
    }),
    ('Pod::Usage', '1.68', {
        'source_tmpl': 'Pod-Usage-1.68.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR/'],
    }),
    ('File::Temp', '0.2304', {
        'source_tmpl': 'File-Temp-0.2304.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'],
    }),
    ('Digest::MD5', '2.54', {
        'source_tmpl': 'Digest-MD5-2.54.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'],
    }),
    ('File::Spec', '3.62', {
        'source_tmpl': 'PathTools-3.62.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS/'],
    }),
    ('JSON', '2.90', {
        'source_tmpl': 'JSON-2.90.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/'],
    }),
    ('Cairo', '1.106', {
        'source_tmpl': 'Cairo-1.106.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'],
    }),
    ('Statistics::PCA', '0.0.1', {
        'source_tmpl': 'Statistics-PCA-0.0.1.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSTH/'],
    }),
    ('MIME::Base64', '3.15', {
        'source_tmpl': 'MIME-Base64-3.15.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'],
    }),
    ('Math::Cephes::Matrix', '0.5304', {
        'source_tmpl': 'Math-Cephes-0.5304.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'],
    }),
    ('Math::MatrixReal', '2.12', {
        'source_tmpl': 'Math-MatrixReal-2.12.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LETO/'],
    }),
    ('Text::SimpleTable', '2.03', {
        'source_tmpl': 'Text-SimpleTable-2.03.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRAMBERG/'],
    }),
    ('Contextual::Return', '0.004008', {
        'source_tmpl': 'Contextual-Return-0.004008.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCONWAY/'],
    }),
    ('Want', '0.26', {
        'source_tmpl': 'Want-0.26.tar.gz',
        'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'],
    }),
]

# this is the script which relies in many extra Perl libraries so we
# verify it's working fine
sanity_check_commands = [('local_perl', '%(installdir)s/prinseq-graphs.pl')]

modextrapaths = {
    'PATH': "",  # add installation dir to PATH
    'PERL5LIB': 'lib/perl5/site_perl/%s/' % (local_perlver)
}

postinstallcmds = [
    # fix shebang line
    "sed -i -e 's|/usr/bin/local_perl|/usr/bin/env\ local_perl|' %(installdir)s/*.pl",
    "chmod +x %(installdir)s/*.pl"  # add execution permission
]

sanity_check_paths = {
    'files': [
        'prinseq-lite.pl',
        'prinseq-graphs.pl',
        'prinseq-graphs-noPCA.pl'],
    'dirs': []}

moduleclass = 'bio'