diff --git a/packages/acpype/package.py b/packages/acpype/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..5b52b2d7cf46a7b85b131f679da2fb3f7a5cddcc
--- /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/package.py b/packages/ambertools/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..8f479cf57433828801aa7f68bc110ac326df2d24
--- /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/package.py b/packages/biobb-analysis/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..68b45f4e28e905d728efcfb65e804af480b10d44
--- /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/package.py b/packages/biobb-chemistry/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..323ec74089f709dc76fe83bb0725d4b60b525010
--- /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/.gitkeep b/packages/biobb-common/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/biobb-common/package.py b/packages/biobb-common/package.py
index 6a5aa81ff00a3327a0e5cd519bde6a48e70824fc..f9996ae582f75b15219379ef07ab6598c962dda2 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/.gitkeep b/packages/biobb-gromacs/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/biobb-gromacs/package.py b/packages/biobb-gromacs/package.py
index c99d49af3ab3f472c62f07d8a1057ab24e22df8a..5e7341bd82aacefd1355d17aa28097bad994f6d7 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/package.py b/packages/biobb-io/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..1b6f1a44d03dc0567dd3d0a4b91aba58e8f6b668
--- /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/package.py b/packages/biobb-model/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..999ce8faa400686e3cdb27bbac86bcfd5a1696d8
--- /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/package.py b/packages/biobb-structure-checking/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..4719d65fa962c06d1d7b9f83f61d5e11f5344db5
--- /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/package.py b/packages/biobb-structure-utils/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..b9ed8b575c0e36f6d1772adeeb8265c8d2216788
--- /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/nest/.gitkeep b/packages/nest/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/packages/nest/package.py b/packages/nest/package.py
index 5eb8ec3fc4ff7d9d3598360994819c790c56c022..54724904c7d33e0ff2bd50acd3c2190389209faf 100644
--- a/packages/nest/package.py
+++ b/packages/nest/package.py
@@ -101,7 +101,7 @@ class Nest(CMakePackage):
depends_on('mpi', when='+mpi')
depends_on('py-mpi4py', when='+python+mpi', type=('run', 'test'))
- depends_on('doxygen', type='build')
+ # depends_on('doxygen', type='build')
depends_on('gsl', when='+gsl')
depends_on('readline', type=('build', 'run', 'test'))
depends_on('ncurses', type=('build', 'run', 'test'))
diff --git a/packages/nglview/package.py b/packages/nglview/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..fda735651d9d1bd0c80dd647d2524a63d72064b1
--- /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/package.py b/packages/simpletraj/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..373665bffa3ed3c29409ca5952a2e6ebe79f7ed4
--- /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 08ff558d4cbc134982513c233578263315c3c632..e1aa0a3732a84e4cb20ef9ebec059f8df22e1c4c 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -1,70 +1,77 @@
spack:
specs:
# Notebook
- - r-irkernel
- - py-ipython
+ - py-ipycanvas
- py-ipykernel
+ - py-ipython
- py-notebook
- - py-ipycanvas
+ - r-irkernel
# "collab"-specific constraint to match ("jupyterlab_widgets") in the base image
- py-ipywidgets@:7.7
# Collab utils
- clb-nb-utils@0.1.0
# EBRAINS tools
- - nest@3.4
+ - apbs@3.4.0
- arbor@0.8.1 +python +mpi
+ - 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
+ - hxtorch@5.0-rc1
+ - nest@3.4
- neuron@8.2.2 +mpi
- - py-pynn@0.11.0 +mpi
+ - nglview@3.0.4
- py-brian2@2.5.0.2
- - py-tvb-data@2.7
- - py-tvb-gdist@2.2
- - py-tvb-library@2.8.1
- - py-tvb-storage@2.8.1
- - py-tvb-framework@2.8.1.1
- - pynn-brainscales@5.0-rc1
- - hxtorch@5.0-rc1
- - py-nestml@5.2.0
- - py-neo@0.12.0
- - py-hdmf@3.4.6
- - py-pynwb@2.1.0
- - py-nixio@1.5.3
- py-cerebrus@1.3.4
- - py-sciunit@0.2.5.1
- - py-quantities@0.14.1
- - py-quantities-scidash@0.12.4.3
- - py-ebrains-kg-core@0.9.14
- py-ebrains-drive@0.5.1
+ - py-ebrains-kg-core@0.9.14
+ - py-efel@4.0.4
+ - py-elephant@0.12.0
- py-fairgraph@0.10.0
- - py-nameparser@1.1.1
- - py-lazyarray@0.5.2
+ - py-frites@0.4.2
- py-hbp-archive@1.1.1
- - py-viziphant@0.3.0
- - py-hippounit@1.3.6
- - py-efel@4.0.4
- py-hbp-neuromorphic-platform@0.10.1
- py-hbp-validation-client@0.8.2
+ - py-hdmf@3.4.6
+ - py-hippounit@1.3.6
+ - py-lazyarray@0.5.2
- py-lfpy@2.3
- - py-elephant@0.12.0
- - py-frites@0.4.2
- - py-snudda@1.4.0
- - py-pyunicore@0.14.1
+ - py-nameparser@1.1.1
+ - py-neo@0.12.0
+ - py-nestml@5.2.0
- py-neuror@1.4.2
- - biobb-common@3.8.1
- - biobb-gromacs@3.8.1
- - apbs@3.4.0
+ - py-neurom@3.2.2
+ - py-nixio@1.5.3
- py-pdb2pqr@3.5.2
- - sda@7.3.3d
- - r-uqsa@2.2
+ - py-pynn@0.11.0 +mpi
+ - py-pynwb@2.1.0
+ - py-pyunicore@0.14.1
+ - py-quantities-scidash@0.12.4.3
+ - py-quantities@0.14.1
+ - py-sciunit@0.2.5.1
+ - py-snudda@1.4.0
+ - py-tvb-data@2.7
+ - py-tvb-framework@2.8.1.1
+ - py-tvb-gdist@2.2
+ - py-tvb-library@2.8.1
+ - py-tvb-storage@2.8.1
+ - py-viziphant@0.3.0
+ - pynn-brainscales@5.0-rc1
- r-rgsl@0.1
- r-sbtabvfgen@0.1
- #- py-version-query
- #- py-cerebstats
- #- py-cerebunit
- #- py-morphounit@1.0.4
- #- py-neurom@1.4.10
- #- py-morphio@3.1.1
+ - r-uqsa@2.2
+ - sda@7.3.3d
+ - simpletraj@0.3
# Workflows (meta-packages)
- wf-uq-akar4@0.1
- wf-multi-area-model@0.1
+ #- py-cerebstats
+ #- py-cerebunit
+ #- py-morphounit@1.0.4
+ #- py-version-query
concretizer:
unify: true