diff options
author | Yifan Zhu <ifanzhu@foxmail.com> | 2018-04-12 13:31:18 -0500 |
---|---|---|
committer | Adam J. Stewart <ajstewart426@gmail.com> | 2018-04-12 13:31:18 -0500 |
commit | fde1e0ecb88fee713b7e9cd6b076f496ec1e8d24 (patch) | |
tree | 3a680e76e64aaaa37b5b174e61425a2027b477e6 | |
parent | 7f46ec49e74d7d3ea3f10dea6cfcea2e61715ae4 (diff) | |
download | spack-fde1e0ecb88fee713b7e9cd6b076f496ec1e8d24.tar.gz spack-fde1e0ecb88fee713b7e9cd6b076f496ec1e8d24.tar.bz2 spack-fde1e0ecb88fee713b7e9cd6b076f496ec1e8d24.tar.xz spack-fde1e0ecb88fee713b7e9cd6b076f496ec1e8d24.zip |
supernova: new package (#7719)
* runing a test
* supernova: new package
* removed with working_dir line
-rw-r--r-- | var/spack/repos/builtin/packages/supernova/package.py | 65 |
1 files changed, 65 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/supernova/package.py b/var/spack/repos/builtin/packages/supernova/package.py new file mode 100644 index 0000000000..3e6ac97bc2 --- /dev/null +++ b/var/spack/repos/builtin/packages/supernova/package.py @@ -0,0 +1,65 @@ +############################################################################## +# 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 * +from distutils.dir_util import copy_tree +import os + + +class Supernova(Package): + """Supernova is a software package for de novo assembly from Chromium + Linked-Reads that are made from a single whole-genome library from an + individual DNA source. + + A key feature of Supernova is that it creates diploid assemblies, thus + separately representing maternal and paternal chromosomes over very long + distances. Almost all other methods instead merge homologous chromosomes + into single incorrect 'consensus' sequences. Supernova is the only + practical method for creating diploid assemblies of large genomes. + + To install this package, you will need to go to the supernova download + page of supernova, register with your email address and download + supernova yourself. Spack will search your current directory for the + download file. Alternatively, add this file yo 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 = "https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome" + + version('2.0.1', '3697ce043c798fcb672fe0a66c56d6f0') + + depends_on('bcl2fastq2') + + def url_for_version(self, version): + return "file://{0}/supernova-{1}.tar.gz".format(os.getcwd(), version) + + def setup_environment(self, spack_env, run_env): + run_env.prepend_path('PATH', self.prefix) + + def install(self, spec, prefix): + rm = which('rm') + # remove the broken symlinks + rm('anaconda-cs/2.2.0-anaconda-cs-c7/lib/libtcl.so', + 'anaconda-cs/2.2.0-anaconda-cs-c7/lib/libtk.so') + copy_tree('.', prefix, preserve_symlinks=1) |