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| author | Yifan Zhu <ifanzhu@foxmail.com> | 2018-01-09 22:07:05 -0600 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2018-01-09 22:07:05 -0600 |
| commit | f498f52a2d5b14661e908df8fc05d104055ddafa (patch) | |
| tree | 28c3ec89a7ee09285ba53636c25d8dc2552d3bba /var | |
| parent | 15111177a2a62139d02d9aff257e577fb9cf2fdc (diff) | |
| download | spack-f498f52a2d5b14661e908df8fc05d104055ddafa.tar.gz spack-f498f52a2d5b14661e908df8fc05d104055ddafa.tar.bz2 spack-f498f52a2d5b14661e908df8fc05d104055ddafa.tar.xz spack-f498f52a2d5b14661e908df8fc05d104055ddafa.zip | |
casper: new package (#6873)
* 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
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/casper/package.py | 49 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/jellyfish/package.py | 7 |
2 files changed, 54 insertions, 2 deletions
diff --git a/var/spack/repos/builtin/packages/casper/package.py b/var/spack/repos/builtin/packages/casper/package.py new file mode 100644 index 0000000000..170bdaecef --- /dev/null +++ b/var/spack/repos/builtin/packages/casper/package.py @@ -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) diff --git a/var/spack/repos/builtin/packages/jellyfish/package.py b/var/spack/repos/builtin/packages/jellyfish/package.py index e6d65838a1..f5e62a828e 100644 --- a/var/spack/repos/builtin/packages/jellyfish/package.py +++ b/var/spack/repos/builtin/packages/jellyfish/package.py @@ -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')) |