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Diffstat (limited to 'var/spack/repos/builtin/packages/supernova/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/supernova/package.py | 45 |
1 files changed, 45 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..ed7b85405d --- /dev/null +++ b/var/spack/repos/builtin/packages/supernova/package.py @@ -0,0 +1,45 @@ +# 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 * +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') + install_tree('.', prefix) |