# 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 = 'MakeCp'

name = "segemehl"
version = "0.2.0"

homepage = 'http://www.bioinf.uni-leipzig.de/Software/segemehl/'
description = """ segemehl is a software to map short sequencer reads to reference genomes.
 Unlike other methods, segemehl is able to detect not only mismatches but also insertions
 and deletions. Furthermore, segemehl is not limited to a specific read length and is able
 to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching
 strategy based on enhanced local_suffix arrays (ESA). Segemehl now supports the SAM format, reads
 gziped queries to save both disk and memory space and allows bisulfite sequencing mapping
 and split read mapping. """

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

source_urls = ['http://www.bioinf.uni-leipzig.de/Software/segemehl/']
sources = ['%s_%s.tar.gz' % (name, version.replace('.', '_'))]

parallel = 1

dependencies = [
    ('ncurses', '5.9'),
    ('zlib', '1.2.8'),
]

files_to_copy = [(["lack.x", "segemehl.x", "testrealign.x"], "bin")]

sanity_check_paths = {
    'files': ["bin/%s" % x for x in ["lack.x", "segemehl.x", "testrealign.x"]],
    'dirs': ["."]
}

moduleclass = 'bio'
