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casper: new package (#6873)

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* casper: create package

* jellyfish: added version 2.2.7

* casper: new package

* casper: depends on jellyfish 2.2.3 or higher

* casper: moved depends_on above install

* casper: updated package.py

* fixing download url for 1.11.1

* casper: set up environment

* casper: add conflicts gcc@7.1.0, cannot install with 7.1.0

* capser: flake8 error corrcted

* casper: create package

* jellyfish: added version 2.2.7

* casper: new package

* casper: depends on jellyfish 2.2.3 or higher

* casper: moved depends_on above install

* casper: updated package.py

* fixing download url for 1.11.1

* casper: set up environment

* casper: add conflicts gcc@7.1.0, cannot install with 7.1.0

* capser: flake8 error corrcted
This commit is contained in:
Yifan Zhu 2018-01-09 22:07:05 -06:00 committed by Adam J. Stewart
parent 15111177a2
commit f498f52a2d
2 changed files with 54 additions and 2 deletions
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49
var/spack/repos/builtin/packages/casper/package.py Normal file
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@ -0,0 +1,49 @@
##############################################################################
# Copyright (c) 2013-2017, 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 *
import distutils.dir_util
class Casper(MakefilePackage):
"""CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art
merging tool in terms of accuracy and robustness. Using this
sophisticated merging method, we could get elongated reads from the
forward and reverse reads."""
homepage = "http://best.snu.ac.kr/casper/index.php?name=main"
url = "http://best.snu.ac.kr/casper/program/casper_v0.8.2.tar.gz"
version('0.8.2', '9e83d32ff46b876f33eb1d7b545ec9c2')
depends_on('jellyfish@2.2.3:')
depends_on('boost')
conflicts('%gcc@7.1.0')
def install(self, spec, prefix):
distutils.dir_util.copy_tree(".", prefix)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PATH', self.spec.prefix)

7
var/spack/repos/builtin/packages/jellyfish/package.py
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@ -30,9 +30,12 @@ class Jellyfish(AutotoolsPackage):
DNA."""
homepage = "http://www.cbcb.umd.edu/software/jellyfish/"
url = "http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz"
url = "https://github.com/gmarcais/Jellyfish/releases/download/v2.2.7/jellyfish-2.2.7.tar.gz"
list_url = "http://www.cbcb.umd.edu/software/jellyfish/"
version('1.1.11', 'dc994ea8b0896156500ea8c648f24846')
version('2.2.7', 'f741192d9061f28e34cb67c86a1027ab')
version('1.1.11', 'dc994ea8b0896156500ea8c648f24846',
url='http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz')
depends_on('perl', type=('build', 'run'))
depends_on('python', type=('build', 'run'))