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67 lines
2.1 KiB
Plaintext
67 lines
2.1 KiB
Plaintext
##
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# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
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#
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# Copyright:: Copyright 2017 University of Geneva
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# Authors:: Yann Sagon <yann.sagon@unige.ch>
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# License:: MIT/GPL
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# $Id$
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#
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##
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easyblock = 'ConfigureMake'
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name = 'MaSuRCA'
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version = '4.0.7'
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versionsuffix = '-Perl-%(perlver)s'
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homepage = 'http://www.genome.umd.edu/masurca.html'
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description = '''MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph
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and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing
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only short reads from Illumina sequencing or a mixture of short reads and long reads
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(Sanger, 454, Pacbio and Nanopore).'''
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toolchain = {'name': 'foss', 'version': '2020a'}
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# need a temporary url to download it. Do it manually here:
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# http://www.genome.umd.edu/masurca_form.html
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source_urls = ['https://github.com/alekseyzimin/masurca/releases/download/v%(version)s']
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sources = ['%(name)s-%(version)s.tar.gz']
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checksums = ['6ad1c06396cc1bd6025d37f0fcce617633c57d414954cdc7dd7c70eec8a09154']
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dependencies = [
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('libreadline', '8.0'),
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('Tcl', '8.6.10'),
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('Boost', '1.72.0'),
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('zlib', '1.2.11'),
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('Perl', '5.30.2'),
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('bzip2', '1.0.8'),
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]
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buildopts = "install-special"
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start_dir = "global-1"
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postinstallcmds = [
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# fix location of 'bin' in install prefix in runCA and runCA-dedupe scripts
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# escaping single quotes within single quotes is tricky, so we use $'...' to use ANSI C-like escaping
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"sed -i $'s|^$bin =.*|$bin = \"$ENV{\'EBROOTMASURCA\'}/bin\";|g' %(installdir)s/bin/runCA",
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"sed -i $'s|^$bin =.*|$bin = \"$ENV{\'EBROOTMASURCA\'}/bin\";|g' %(installdir)s/bin/runCA-dedupe",
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# fix hardcoded path in masurca script, just point back to 'bin' subdirectory instead
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"sed -i 's@../CA8/Linux-amd64/bin@../bin@g' %(installdir)s/bin/masurca",
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# commands to install built-in version of Flye
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"cd ../Flye && make && cp -a ../Flye %(installdir)s",
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]
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sanity_check_paths = {
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'files': ['bin/masurca', 'Flye/bin/flye'],
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'dirs': ['include', 'lib'],
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}
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sanity_check_commands = [
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"masurca --help",
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"runCA --help",
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]
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moduleclass = 'bio'
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