1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
|
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class SoapdenovoTrans(MakefilePackage):
"""SOAPdenovo-Trans is a de novo transcriptome assembler basing on the
SOAPdenovo framework, adapt to alternative splicing and different
expression level among transcripts."""
homepage = "http://soap.genomics.org.cn/SOAPdenovo-Trans.html"
url = "https://github.com/aquaskyline/SOAPdenovo-Trans/archive/1.0.4.tar.gz"
version('1.0.4', 'a3b00b0f743b96141c4d5f1b49f2918c')
build_directory = 'src'
def edit(self, spec, prefix):
with working_dir(self.build_directory):
makefile = FileFilter('Makefile')
makefile.filter('CFLAGS= -O3 -fomit-frame-pointer -static',
'CFLAGS= -O3 -fomit-frame-pointer')
def build(self, spec, prefix):
with working_dir(self.build_directory):
make()
make('127mer=1', parallel=False)
def install(self, spec, prefix):
install_tree('.', prefix.bin)
|
