# 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 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'
