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+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+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)