From 528a8359ff2692504d580d6fdb7b7d50d923b61a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dani=20Beltr=C3=A1n?= <daniel.beltran@irbbarcelona.org>
Date: Fri, 9 Jun 2023 17:34:16 +0200
Subject: [PATCH] add/update spack packages for several BioBBs and their
dependencies
---
packages/acpype/.gitkeep | 0
packages/acpype/package.py | 21 ++++++
packages/ambertools/.gitkeep | 0
packages/ambertools/package.py | 79 ++++++++++++++++++++
packages/biobb-analysis/.gitkeep | 0
packages/biobb-analysis/package.py | 21 ++++++
packages/biobb-chemistry/.gitkeep | 0
packages/biobb-chemistry/package.py | 22 ++++++
packages/biobb-common/package.py | 16 ++--
packages/biobb-gromacs/package.py | 17 +----
packages/biobb-io/.gitkeep | 0
packages/biobb-io/package.py | 16 ++++
packages/biobb-model/.gitkeep | 0
packages/biobb-model/package.py | 17 +++++
packages/biobb-structure-checking/.gitkeep | 0
packages/biobb-structure-checking/package.py | 20 +++++
packages/biobb-structure-utils/.gitkeep | 0
packages/biobb-structure-utils/package.py | 17 +++++
packages/nglview/.gitkeep | 0
packages/nglview/package.py | 23 ++++++
packages/simpletraj/.gitkeep | 0
packages/simpletraj/package.py | 19 +++++
spack.yaml | 12 ++-
23 files changed, 274 insertions(+), 26 deletions(-)
create mode 100644 packages/acpype/.gitkeep
create mode 100644 packages/acpype/package.py
create mode 100644 packages/ambertools/.gitkeep
create mode 100644 packages/ambertools/package.py
create mode 100644 packages/biobb-analysis/.gitkeep
create mode 100644 packages/biobb-analysis/package.py
create mode 100644 packages/biobb-chemistry/.gitkeep
create mode 100644 packages/biobb-chemistry/package.py
create mode 100644 packages/biobb-io/.gitkeep
create mode 100644 packages/biobb-io/package.py
create mode 100644 packages/biobb-model/.gitkeep
create mode 100644 packages/biobb-model/package.py
create mode 100644 packages/biobb-structure-checking/.gitkeep
create mode 100644 packages/biobb-structure-checking/package.py
create mode 100644 packages/biobb-structure-utils/.gitkeep
create mode 100644 packages/biobb-structure-utils/package.py
create mode 100644 packages/nglview/.gitkeep
create mode 100644 packages/nglview/package.py
create mode 100644 packages/simpletraj/.gitkeep
create mode 100644 packages/simpletraj/package.py
diff --git a/packages/acpype/.gitkeep b/packages/acpype/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/packages/acpype/package.py b/packages/acpype/package.py
new file mode 100644
index 00000000..5b52b2d7
--- /dev/null
+++ b/packages/acpype/package.py
@@ -0,0 +1,21 @@
+from spack import *
+
+class Acpype(PythonPackage):
+ """A tool based in Python to use Antechamber to generate topologies for chemical
+ compounds and to interface with others python applications like CCPN and ARIA"""
+
+ # Homepage and download url
+ homepage = "https://github.com/alanwilter/acpype"
+ git = 'https://github.com/alanwilter/acpype.git'
+
+ # Set the gitlab accounts of this package maintainers
+ maintainers = ['dbeltran']
+
+ # Versions
+ version('2022.7.21', branch='master')
+
+ # Dependencies
+ depends_on('python@3.8:', type=('build', 'run'))
+ depends_on('ambertools')
+ depends_on('openbabel')
+ depends_on('py-poetry-core')
diff --git a/packages/ambertools/.gitkeep b/packages/ambertools/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/packages/ambertools/package.py b/packages/ambertools/package.py
new file mode 100644
index 00000000..8f479cf5
--- /dev/null
+++ b/packages/ambertools/package.py
@@ -0,0 +1,79 @@
+from spack import *
+
+class Ambertools (CMakePackage):
+ """AmberTools is a free, useful standalone package and a prerequisite for installing Amber itself.
+ The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL).
+ A few components are included that are in the public domain or which have other, open-source, licenses.
+ The libsander and libpbsa libraries use the LGPL license."""
+
+ # Set the homepage and download url
+ homepage = "https://ambermd.org/AmberTools.php"
+ url = "https://ambermd.org/downloads/AmberTools22jlmrcc.tar.bz2"
+
+ # Set the gitlab accounts of this package maintainers
+ maintainers = ['dbeltran', 'elmath']
+
+ version('22jlmrcc', sha256='1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121')
+
+ # Dependencies
+ depends_on("flex", type="build") # This is necessary for sure (experimentally tested)
+ depends_on("bison", type="build") # This is necessary for sure (experimentally tested)
+ depends_on("tcsh", type="build")
+ depends_on("zlib", type=("build", "run"))
+ depends_on("bzip2", type=("build", "run"))
+ depends_on("blas", type=("build", "run"))
+ depends_on("lapack", type=("build", "run"))
+ depends_on("arpack-ng", type=("build", "run"))
+ depends_on("netcdf-c", type=("build", "run"))
+ depends_on("netcdf-fortran", type=("build", "run"))
+ depends_on("fftw", type=("build", "run"))
+ depends_on("readline", type=("build", "run"))
+ depends_on("netlib-xblas~plain_blas", type=("build", "run"))
+ # specific variants needed for boost - from the build log "Could NOT find Boost (missing: thread system program_options iostreams regex timer chrono filesystem graph)"
+ depends_on("boost+thread+system+program_options+iostreams+regex+timer+chrono+filesystem+graph", type=("build", "run"))
+
+ # Python dependencies
+ # WARNING: If a python 3.8 version is already installed in spack then the '+tkinter' variant makes spack ignore the version
+ # WARNING: Spack may try to install the preferred python version (i.e. python 3.10.8)
+ # WARNING: The soultion is uninstall python and reinstall with this variant
+ depends_on('python@3.8: +tkinter', type=('build', 'run'))
+ depends_on("py-numpy", type=("build", "run"))
+ depends_on("py-matplotlib", type=("build", "run"))
+ depends_on("py-scipy", type=("build", "run"))
+
+ def cmake_args(self):
+ # Translated from ambertools build/run_cmake script
+ # We also add the TRUST_SYSTEM_LIBS argument that is mentioned in the ambertools CMake guide
+ # https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Guide-to-Options
+ args = [
+ self.define("COMPILER", "GNU"),
+ self.define("MPI", False),
+ self.define("CUDA", False),
+ self.define("INSTALL_TESTS", True),
+ self.define("DOWNLOAD_MINICONDA", False),
+ self.define("TRUST_SYSTEM_LIBS", True),
+ # This is to avoid the x11 (X11_Xext_LIB) error
+ # It is equivalent to the '-noX11' flag accoridng to the docs:
+ # https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
+ self.define("BUILD_GUI", False)
+ ]
+ return args
+
+ def setup_run_environment(self, env):
+ env.set("AMBER_PREFIX", self.prefix)
+ env.set("AMBERHOME", self.prefix)
+
+ def setup_build_environment(self, env):
+ env.set("AMBER_PREFIX", self.prefix)
+ env.set("AMBERHOME", self.prefix)
+
+ @run_after('install')
+ @on_package_attributes(run_tests=True)
+ def check_install(self):
+ make("test.serial")
+
+ # temporarily copy netcdf.h header file to netcdf-fortran/include to pass the Ambertools cmake check (quickest fix, will probably cause problems, needs to change)
+ @run_before("cmake")
+ def fix_check(self):
+ cp = Executable("cp")
+ cp(self.spec["netcdf-c"].headers.directories[0]+"/netcdf.h", self.spec["netcdf-fortran"].headers.directories[0])
diff --git a/packages/biobb-analysis/.gitkeep b/packages/biobb-analysis/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/packages/biobb-analysis/package.py b/packages/biobb-analysis/package.py
new file mode 100644
index 00000000..68b45f4e
--- /dev/null
+++ b/packages/biobb-analysis/package.py
@@ -0,0 +1,21 @@
+from spack import *
+
+class BiobbAnalysis(PythonPackage):
+ """Biobb_analysis is the Biobb module collection to perform analysis
+ of molecular dynamics simulations"""
+
+ # Homepage and download url
+ homepage = "https://github.com/bioexcel/biobb_analysis"
+ git = 'https://github.com/bioexcel/biobb_analysis.git'
+
+ # Set the gitlab accounts of this package maintainers
+ maintainers = ['dbeltran']
+
+ # Versions
+ version('4.0.1', branch='master')
+
+ # Dependencies
+ depends_on('python@3.8:', type=('build', 'run'))
+ depends_on('biobb-common')
+ depends_on('gromacs')
+ depends_on('ambertools')
diff --git a/packages/biobb-chemistry/.gitkeep b/packages/biobb-chemistry/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/packages/biobb-chemistry/package.py b/packages/biobb-chemistry/package.py
new file mode 100644
index 00000000..323ec740
--- /dev/null
+++ b/packages/biobb-chemistry/package.py
@@ -0,0 +1,22 @@
+from spack import *
+
+class BiobbChemistry(PythonPackage):
+ """Biobb_chemistry is the Biobb module collection to perform chemistry
+ over molecular dynamics simulations."""
+
+ # Homepage and download url
+ homepage = "https://github.com/bioexcel/biobb_chemistry"
+ git = 'https://github.com/bioexcel/biobb_chemistry.git'
+
+ # Set the gitlab accounts of this package maintainers
+ maintainers = ['dbeltran']
+
+ # Versions
+ version('4.0.0', branch='master')
+
+ # Dependencies
+ depends_on('python@3.8:', type=('build', 'run'))
+ depends_on('biobb-common')
+ depends_on('openbabel')
+ depends_on('ambertools')
+ depends_on('acpype')
diff --git a/packages/biobb-common/package.py b/packages/biobb-common/package.py
index 6a5aa81f..f9996ae5 100644
--- a/packages/biobb-common/package.py
+++ b/packages/biobb-common/package.py
@@ -1,9 +1,3 @@
-# Copyright 2013-2023 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 BiobbCommon(PythonPackage):
@@ -11,17 +5,17 @@ class BiobbCommon(PythonPackage):
# Homepage and download url
homepage = "https://github.com/bioexcel/biobb_common"
- url = "https://github.com/bioexcel/biobb_common/archive/refs/tags/v3.8.1.tar.gz"
+ git = 'https://github.com/bioexcel/biobb_common.git'
+ # Set the gitlab accounts of this package maintainers
maintainers = ['dbeltran']
# Versions
- version('3.8.1', sha256='b6c939c1445ea2f8282e491e0414cc15f4934466ca24ecd77e24cef2e7df49e4')
+ version('4.0.0', branch='master')
# Dependencies
- depends_on('python@3.8:')
- depends_on('py-setuptools', type=('build'))
+ depends_on('py-setuptools')
+ depends_on('python@3.8:', type=('build', 'run'))
depends_on('py-pyyaml', type=('build', 'run'))
depends_on('py-requests', type=('build', 'run'))
depends_on('py-biopython@1.78:1.80', type=('build', 'run'))
-
diff --git a/packages/biobb-gromacs/package.py b/packages/biobb-gromacs/package.py
index c99d49af..5e7341bd 100644
--- a/packages/biobb-gromacs/package.py
+++ b/packages/biobb-gromacs/package.py
@@ -1,9 +1,3 @@
-# Copyright 2013-2023 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 BiobbGromacs(PythonPackage):
@@ -12,15 +6,12 @@ class BiobbGromacs(PythonPackage):
# Homepage and download url
homepage = "https://github.com/bioexcel/biobb_gromacs"
- url = "https://github.com/bioexcel/biobb_gromacs/archive/refs/tags/v3.8.1.tar.gz"
-
- maintainers = ['dbeltran']
+ git = 'https://github.com/bioexcel/biobb_gromacs.git'
# Versions
- version('3.8.1', sha256='6da49b691b14a8bcf7ffca08c898fe9affd258ca2f8c7be4981df840a6907efa')
+ version('4.0.0', branch='master')
# Dependencies
- depends_on('python@3.8:')
- depends_on('py-setuptools', type=('build'))
- depends_on('biobb-common@3.8.1', type=('build', 'run'), when='@3.8.1')
+ depends_on('python@3.8:', type=('build', 'run'))
+ depends_on('biobb-common')
depends_on('gromacs')
diff --git a/packages/biobb-io/.gitkeep b/packages/biobb-io/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/packages/biobb-io/package.py b/packages/biobb-io/package.py
new file mode 100644
index 00000000..1b6f1a44
--- /dev/null
+++ b/packages/biobb-io/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class BiobbIo(PythonPackage):
+ """Biobb_io is the Biobb module collection to fetch data to be
+ consumed by the rest of the Biobb building blocks"""
+
+ # Homepage and download url
+ homepage = "https://github.com/bioexcel/biobb_io"
+ git = 'https://github.com/bioexcel/biobb_io.git'
+
+ # Versions
+ version('4.0.0', branch='master')
+
+ # Dependencies
+ depends_on('biobb-common')
+ depends_on('python@3.8:', type=('build', 'run'))
diff --git a/packages/biobb-model/.gitkeep b/packages/biobb-model/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/packages/biobb-model/package.py b/packages/biobb-model/package.py
new file mode 100644
index 00000000..999ce8fa
--- /dev/null
+++ b/packages/biobb-model/package.py
@@ -0,0 +1,17 @@
+from spack import *
+
+class BiobbModel(PythonPackage):
+ """Biobb_model is the Biobb module collection to check and model 3d structures,
+ create mutations or reconstruct missing atoms"""
+
+ # Homepage and download url
+ homepage = "https://github.com/bioexcel/biobb_model"
+ git = 'https://github.com/bioexcel/biobb_model.git'
+
+ # Versions
+ version('4.0.0', branch='master')
+
+ # Dependencies
+ depends_on('python@3.8:', type=('build', 'run'))
+ depends_on('biobb-common')
+ depends_on('biobb-structure-checking')
diff --git a/packages/biobb-structure-checking/.gitkeep b/packages/biobb-structure-checking/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/packages/biobb-structure-checking/package.py b/packages/biobb-structure-checking/package.py
new file mode 100644
index 00000000..4719d65f
--- /dev/null
+++ b/packages/biobb-structure-checking/package.py
@@ -0,0 +1,20 @@
+from spack import *
+
+class BiobbStructureChecking(PythonPackage):
+ """Biobb_structure_checking performs a checking of the quality of a
+ 3D structure intended to facilitate the setup of molecular dynamics
+ simulation of protein or nucleic acids systems"""
+
+ # Homepage and download url
+ homepage = "https://github.com/bioexcel/biobb_structure_checking"
+ git = 'https://github.com/bioexcel/biobb_structure_checking.git'
+
+ # Versions
+ version('3.12.1', branch='master')
+
+ # Dependencies
+ depends_on('py-setuptools')
+ depends_on('python@3.8:', type=('build', 'run'))
+ depends_on('py-psutil', type=('build', 'run'))
+ depends_on('py-numpy', type=('build', 'run'))
+ depends_on('py-biopython@1.78:1.80', type=('build', 'run'))
diff --git a/packages/biobb-structure-utils/.gitkeep b/packages/biobb-structure-utils/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/packages/biobb-structure-utils/package.py b/packages/biobb-structure-utils/package.py
new file mode 100644
index 00000000..b9ed8b57
--- /dev/null
+++ b/packages/biobb-structure-utils/package.py
@@ -0,0 +1,17 @@
+from spack import *
+
+class BiobbStructureUtils(PythonPackage):
+ """Biobb_structure_utils is the Biobb module collection to modify
+ or extract information from a PDB structure file."""
+
+ # Homepage and download url
+ homepage = "https://github.com/bioexcel/biobb_structure_utils"
+ git = 'https://github.com/bioexcel/biobb_structure_utils.git'
+
+ # Versions
+ version('4.0.0', branch='master')
+
+ # Dependencies
+ depends_on('python@3.8:', type=('build', 'run'))
+ depends_on('biobb-common')
+ depends_on('biobb-structure-checking')
diff --git a/packages/nglview/.gitkeep b/packages/nglview/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/packages/nglview/package.py b/packages/nglview/package.py
new file mode 100644
index 00000000..fda73565
--- /dev/null
+++ b/packages/nglview/package.py
@@ -0,0 +1,23 @@
+from spack import *
+
+class Nglview(PythonPackage):
+ """An IPython/Jupyter widget to interactively view molecular structures and trajectories.
+ Utilizes the embeddable NGL Viewer for rendering."""
+
+ # Homepage and download url
+ homepage = "https://github.com/nglviewer/nglview"
+ git = 'https://github.com/nglviewer/nglview.git'
+
+ # Set the gitlab accounts of this package maintainers
+ maintainers = ['dbeltran']
+
+ # Versions
+ version('3.0.4', branch='master')
+
+ # Dependencies
+ depends_on('python@3.8:', type=('build', 'run'))
+ depends_on('py-setuptools')
+ depends_on('py-jupyter-packaging')
+ depends_on('py-versioneer')
+ depends_on('py-numpy', type=('run'))
+ depends_on('py-ipywidgets', type=('run'))
\ No newline at end of file
diff --git a/packages/simpletraj/.gitkeep b/packages/simpletraj/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/packages/simpletraj/package.py b/packages/simpletraj/package.py
new file mode 100644
index 00000000..373665bf
--- /dev/null
+++ b/packages/simpletraj/package.py
@@ -0,0 +1,19 @@
+from spack import *
+
+class Simpletraj(PythonPackage):
+ """Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD."""
+
+ # Homepage and download url
+ homepage = "https://github.com/arose/simpletraj"
+ git = 'https://github.com/arose/simpletraj.git'
+
+ # Set the gitlab accounts of this package maintainers
+ maintainers = ['dbeltran']
+
+ # Versions
+ version('0.3', branch='master')
+
+ # Dependencies
+ depends_on('python@3.8:', type=('build', 'run'))
+ depends_on('py-setuptools')
+ depends_on('py-numpy')
diff --git a/spack.yaml b/spack.yaml
index 08ff558d..37239726 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -49,8 +49,16 @@ spack:
- py-snudda@1.4.0
- py-pyunicore@0.14.1
- py-neuror@1.4.2
- - biobb-common@3.8.1
- - biobb-gromacs@3.8.1
+ - biobb-analysis@4.0.1
+ - biobb-chemistry@4.0.0
+ - biobb-common@4.0.0
+ - biobb-gromacs@4.0.0
+ - biobb-io@4.0.0
+ - biobb-model@4.0.0
+ - biobb-structure-checking@3.12.1
+ - biobb-structure-utils@4.0.0
+ - nglview@3.0.4
+ - simpletraj@0.3
- apbs@3.4.0
- py-pdb2pqr@3.5.2
- sda@7.3.3d
--
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