summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorGeorge Hartzell <hartzell@alerce.com>2017-08-03 09:32:44 -0700
committerAdam J. Stewart <ajstewart426@gmail.com>2017-08-03 11:32:44 -0500
commit687904c7144418597ed04dfc793961ae347816a4 (patch)
treee9761fe6389515cb4b71556ed0cd600f598cde76
parent963eb99b7f7306d69a755ddd50bd8b8fca0076c3 (diff)
downloadspack-687904c7144418597ed04dfc793961ae347816a4.tar.gz
spack-687904c7144418597ed04dfc793961ae347816a4.tar.bz2
spack-687904c7144418597ed04dfc793961ae347816a4.tar.xz
spack-687904c7144418597ed04dfc793961ae347816a4.zip
New package for canu (#4937)
* Add package for canu There's a top-level perl script, which is touched up to use a spack-built perl instead of `#!/usr/bin/env perl`. It's self-contained, it uses `FindBin` to locate it's libaries. * Add dependency on gnuplot I noticed a hidden mention of the use of gnuplot in the docs. This adds the dependency. * Tighten dependencies, flake8 cleanup gnuplot is a run dependency. jdk is a run dependency. perl is a run dependency. Make flake8 happy.
-rw-r--r--var/spack/repos/builtin/packages/canu/package.py61
1 files changed, 61 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/canu/package.py b/var/spack/repos/builtin/packages/canu/package.py
new file mode 100644
index 0000000000..fd6acfec0f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/canu/package.py
@@ -0,0 +1,61 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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/llnl/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 *
+
+
+class Canu(MakefilePackage):
+ """A single molecule sequence assembler for genomes large and
+ small."""
+
+ homepage = "http://canu.readthedocs.io/"
+ url = "https://github.com/marbl/canu/archive/v1.5.tar.gz"
+
+ version('1.5', '65df275baa28ecf11b15dfd7343361e3')
+
+ depends_on('gnuplot', type='run')
+ depends_on('jdk', type='run')
+ depends_on('perl', type='run')
+
+ build_directory = 'src'
+
+ def patch(self):
+ # Use our perl, not whatever is in the environment
+ perl = self.spec['perl'].prefix.bin.perl
+ filter_file(r'^#!/usr/bin/env perl',
+ '#!{0}'.format(perl),
+ 'src/pipelines/canu.pl')
+
+ def install(self, spec, prefix):
+ # replicate the Makefile logic here:
+ # https://github.com/marbl/canu/blob/master/src/Makefile#L344
+ uname = which('uname')
+ ostype = uname(output=str).strip()
+ machinetype = uname('-m', output=str).strip()
+ if machinetype == 'x86_64':
+ machinetype = 'amd64'
+ target_dir = '{0}-{1}'.format(ostype, machinetype)
+ bin = join_path(target_dir, 'bin')
+
+ install_tree(bin, prefix.bin)