HiCOPS: add new package (#26767)

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>

2 files changed, 114 insertions, 1 deletions

diff --git a/var/spack/repos/builtin/packages/hicops/package.py b/var/spack/repos/builtin/packages/hicops/package.py
new file mode 100644
index 0000000000..ccd52af0e0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hicops/package.py
@@ -0,0 +1,113 @@
+# Copyright 2013-2022 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 *
+
+
+class Hicops(CMakePackage):
+    """HiCOPS is a software framework for accelerating database peptide search
+    workflows on supercomputers. HiCOPS provided algorithm-independent
+    parallelizations and optimizations can be extended into new HPC database search
+    algorithms or scalably accelerate the existing ones.
+    """
+
+    homepage = "https://hicops.github.io/index"
+    git = "https://github.com/hicops/hicops.git"
+    maintainers = ['pcdslab', 'mhaseeb123', 'nessiecancode']
+
+    version('release', branch='release')
+    version('develop', branch='develop')
+
+    # Build Options
+    variant('mpi', default=True,
+            description='Enable MPI support.')
+    variant('timemory', default=False,
+            description='Enable timemory interface. Requires timemory '
+                        'installation.')
+    variant('mpip', default=False,
+            description='Enables the MPIP data_tracker via Timemory. '
+                        'Requires timemory installation.')
+    variant('tailfit', default=True,
+            description='Use the tailfit method instead of Gumbelfit '
+                        'for e-value computation.')
+    variant('progress', default=True,
+            description='Display HiCOPS progress marks.')
+    variant('seqlen', default='60',
+            description='Allowed maximum peptide sequence length.',
+            values=int, multi=False)
+    variant('qalen', default='100',
+            description='Maximum number of top K peaks to keep when '
+                        'spectrum preprocess.', values=int,
+            multi=False)
+    variant('qchunk', default='10000',
+            description='Max size of each batch extracted from the '
+                        'dataset.', values=int, multi=False)
+    variant('hyperscore', default='100',
+            description='Maximum allowed hyperscore computed.',
+            values=int, multi=False)
+    variant('shdpeaks', default='80',
+            description='Maximum shared b- or y-ions allowed.',
+            values=int, multi=False)
+    variant('cxx_std', default='14',
+            description='C++ standard', values=('14', '17'),
+            multi=False)
+
+    depends_on('py-numpy')
+    depends_on('py-python-dateutil')
+    depends_on('py-setuptools')
+    depends_on('py-bottleneck')
+    depends_on('py-pyparsing')
+    depends_on('py-subprocess32')
+    depends_on('py-six')
+    depends_on('py-setuptools-scm')
+    depends_on('py-et-xmlfile')
+    depends_on('py-argparse')
+    depends_on('py-cython')
+    depends_on('py-cycler')
+    depends_on('py-pytz')
+    depends_on('py-kiwisolver')
+    depends_on('py-numexpr')
+    depends_on('py-matplotlib')
+    depends_on('py-jdcal')
+    depends_on('py-pandas')
+    depends_on('py-openpyxl')
+    depends_on('python@3.7:3.9')
+    depends_on('boost')
+    depends_on('mpich')
+    depends_on('git', type='build', when='@release')
+    depends_on('git', type='build', when='@develop')
+    depends_on('cmake@3.11:', type='build')
+    depends_on('pkgconf', type='build')
+    # TODO: Add timemory and mpip depends_on()
+
+    conflicts('+timemory')
+    # Build failing when added. Creating a conflict as a workaround
+    conflicts('%gcc@:7.2.0')
+    conflicts('+mpip -timemory')
+    conflicts('+mpip -mpi')
+
+    def setup_run_environment(self, env):
+        env.prepend_path('PATH', self.prefix.tools)
+        env.prepend_path('PATH', self.prefix.bin.tools)
+        env.set('HICOPS_INSTALL', self.prefix)
+        env.prepend_path('INCLUDE', self.prefix.include)
+
+    def cmake_args(self):
+        args = [
+            self.define('USE_MPI', True),
+            self.define('CMAKE_INSTALL_PREFIX', self.prefix),
+            self.define_from_variant('USE_TIMEMORY', 'timemory'),
+            self.define_from_variant('USE_MPIP_LIBRARY', 'mpip'),
+            self.define_from_variant('TAILFIT', 'tailfit'),
+            self.define_from_variant('PROGRESS', 'progress'),
+            self.define_from_variant('MAX_SEQ_LEN', 'seqlen'),
+            self.define_from_variant('QALEN', 'qalen'),
+            self.define_from_variant('QCHUNK', 'qchunk'),
+            self.define_from_variant('MAX_HYPERSCORE', 'hyperscore'),
+            self.define_from_variant('MAX_SHDPEAKS', 'shdpeaks'),
+            self.define_from_variant('CMAKE_CXX_STANDARD', 'cxx_std')
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/lastz/package.py b/var/spack/repos/builtin/packages/lastz/package.py
index f87845b9f8..114dd2faca 100644
--- a/var/spack/repos/builtin/packages/lastz/package.py
+++ b/var/spack/repos/builtin/packages/lastz/package.py
@@ -11,7 +11,7 @@ class Lastz(MakefilePackage):
 
     homepage = "https://lastz.github.io/lastz"
     url      = "https://github.com/lastz/lastz/archive/1.04.00.tar.gz"
-
+    version('1.04.15', sha256='46a5cfb1fd41911a36fce5d3a2721ebfec9146952943b302e78b0dfffddd77f8')
     version('1.04.03', sha256='c58ed8e37c4b0e82492b3a2b3e12447a3c40286fb8358906d19f10b0a713e9f4')
     version('1.04.00', sha256='a4c2c7a77430387e96dbc9f5bdc75874334c672be90f5720956c0f211abf9f5a')