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signalp: new package (#5054)

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* signalp: new package

* fixed homepage

* fixed url and phases

* refixed phase

* improved readability

* making path in execuatble adaptable to new versions
This commit is contained in:
Audrey Thoma 2017-08-11 13:54:12 -05:00 committed by Adam J. Stewart
parent d16f823f9d
commit 056faad3a2
1 changed files with 61 additions and 0 deletions
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var/spack/repos/builtin/packages/signalp/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2016, 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/llnl/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 *
import os
class Signalp(Package):
"""SignalP predicts the presence and location of signal peptide cleavage
sites in amino acid sequences from different organisms: Gram-positive
bacteria, Gram-negative bacteria, and eukaryotes.
Note: A manual download is required for SignalP.
Spack will search your current directory for the download file.
Alternatively, add this file to a mirror so that Spack can find it.
For instructions on how to set up a mirror, see
http://spack.readthedocs.io/en/latest/mirrors.html"""
homepage = "http://www.cbs.dtu.dk/services/SignalP/"
url = "file://{0}/signalp-4.1f.Linux.tar.gz".format(os.getcwd())
version('4.1f', 'a9aeb66259202649c959846f3f4d9744')
depends_on('perl', type=('build', 'run'))
depends_on('gnuplot')
def patch(self):
edit = FileFilter('signalp')
edit.filter("ENV{SIGNALP} = .*",
"ENV{SIGNALP} = '%s'" % self.prefix)
def install(self, spec, prefix):
mkdirp(prefix.share.man)
install('signalp', prefix)
install('signalp.1', prefix.share.man)
install_tree('bin', prefix.bin)
install_tree('lib', prefix.lib)
install_tree('syn', prefix.syn)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PATH', prefix)