From fde1e0ecb88fee713b7e9cd6b076f496ec1e8d24 Mon Sep 17 00:00:00 2001
From: Yifan Zhu <ifanzhu@foxmail.com>
Date: Thu, 12 Apr 2018 13:31:18 -0500
Subject: [PATCH] supernova: new package (#7719)

* runing a test

* supernova: new package

* removed with working_dir line
---
 .../builtin/packages/supernova/package.py     | 65 +++++++++++++++++++
 1 file changed, 65 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/supernova/package.py

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)