From c3f7bd803c006450ba86b22350a30952e6106d76 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Mon, 26 Aug 2024 15:25:42 -0700 Subject: [PATCH] docs: updated software list --- includes/data/software.yml | 251 ++++++++++++++++++---------------- src/docs/software/updates.xml | 153 ++------------------- 2 files changed, 141 insertions(+), 263 deletions(-) diff --git a/includes/data/software.yml b/includes/data/software.yml index d0066c531..58cb1b36b 100644 --- a/includes/data/software.yml +++ b/includes/data/software.yml @@ -5486,19 +5486,39 @@ software_modules: Sequencing platforms., markedDefault: false, versionName: 2.2.1_py36} - name: chemistry packages: - - categories: chemistry, cheminformatics - defaultVersionName: 2018.09.1_py27 - description: RDKit is a collection of cheminformatics and machine-learning software - written in C++ and Python. - package: py-rdkit - url: http://www.rdkit.org + - categories: chemistry, quantum chemistry + defaultVersionName: '7.1' + description: Quantum ESPRESSO is an integrated suite of Open-Source computer + codes for electronic-structure calculations and materials modeling at the + nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. + package: quantum-espresso_gpu + url: https://www.quantum-espresso.org versions: - - {description: RDKit is a collection of cheminformatics and machine-learning - software written in C++ and Python., markedDefault: false, versionName: 2018.09.1_py36} - - {description: RDKit is a collection of cheminformatics and machine-learning - software written in C++ and Python., markedDefault: false, versionName: 2022.09.1_py39} - - {description: RDKit is a collection of cheminformatics and machine-learning - software written in C++ and Python., markedDefault: true, versionName: 2018.09.1_py27} + - description: GPU-accelerated Quantum ESPRESSO using CUDA FORTRAN + family: qe + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '1.1' + - description: Quantum ESPRESSO is an integrated suite of Open-Source computer + codes for electronic-structure calculations and materials modeling at the + nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. + family: qe + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '7.0' + - description: Quantum ESPRESSO is an integrated suite of Open-Source computer + codes for electronic-structure calculations and materials modeling at the + nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. + family: qe + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '7.1' - categories: chemistry, computational chemistry defaultVersionName: 2.6.0 description: Libint computes molecular integrals. @@ -5612,50 +5632,19 @@ software_modules: arch: {gpu: 1} license: {restricted: 1} versionName: 1.95A - - categories: chemistry, computational chemistry - defaultVersionName: 5.4.1 - description: The Vienna Ab initio Simulation Package (VASP) is a computer program - for atomic scale materials modelling, e.g. electronic structure calculations - and quantum-mechanical molecular dynamics, from first principles. - package: vasp - url: https://www.vasp.at + - categories: chemistry, molecular dynamics + defaultVersionName: 1.0.0 + description: A collection of tools for characterizing membrane structure and + dynamics within simulated trajectories of molecular systems. + package: mosaics + url: https://github.com/MOSAICS-NIH/MOSAICS versions: - - description: The Vienna Ab initio Simulation Package (VASP) is a computer - program for atomic scale materials modelling, e.g. electronic structure - calculations and quantum-mechanical molecular dynamics, from first principles. + - description: A collection of tools for characterizing membrane structure and + dynamics within simulated trajectories of molecular systems. markedDefault: false properties: - arch: {gpu: 1} - license: {restricted: 1} parallel: {mpi: 1} - versionName: 6.1.1 - - description: The Vienna Ab initio Simulation Package (VASP) is a computer - program for atomic scale materials modelling, e.g. electronic structure - calculations and quantum-mechanical molecular dynamics, from first principles. - markedDefault: false - properties: - arch: {gpu: 1} - license: {restricted: 1} - parallel: {mpi: 1} - versionName: 6.3.2 - - description: The Vienna Ab initio Simulation Package (VASP) is a computer - program for atomic scale materials modelling, e.g. electronic structure - calculations and quantum-mechanical molecular dynamics, from first principles. - markedDefault: false - properties: - arch: {gpu: 1} - license: {restricted: 1} - parallel: {mpi: 1} - versionName: 6.4.1 - - description: The Vienna Ab initio Simulation Package (VASP) is a computer - program for atomic scale materials modelling, e.g. electronic structure - calculations and quantum-mechanical molecular dynamics, from first principles. - markedDefault: true - properties: - arch: {gpu: 1} - license: {restricted: 1} - parallel: {mpi: 1} - versionName: 5.4.1 + versionName: 1.0.0 - categories: chemistry, docking defaultVersionName: 1.0.2 description: A deep learning framework for molecular docking @@ -5724,6 +5713,18 @@ software_modules: arch: {gpu: 1} license: {restricted: 1} versionName: g16.B01 + - categories: chemistry, x-ray spectroscopy + defaultVersionName: 0.9.80_py312 + description: Larch is a open-source library and set of applications for processing + and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray + fluorescence and diffraction image data from synchrotron beamlines. + package: py-xraylarch + url: https://xraypy.github.io/xraylarch/ + versions: + - {description: Larch is a open-source library and set of applications for processing + and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray + fluorescence and diffraction image data from synchrotron beamlines., markedDefault: false, + versionName: 0.9.80_py312} - categories: chemistry, computational chemistry defaultVersionName: 3.22.1_py39 description: The Atomic Simulation Environment (ASE) is a set of tools and Python @@ -5754,18 +5755,6 @@ software_modules: versions: - {description: APBS solves the equations of continuum electrostatics for large biomolecular assemblages., markedDefault: false, versionName: '1.5'} - - categories: chemistry, x-ray spectroscopy - defaultVersionName: 0.9.80_py312 - description: Larch is a open-source library and set of applications for processing - and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray - fluorescence and diffraction image data from synchrotron beamlines. - package: py-xraylarch - url: https://xraypy.github.io/xraylarch/ - versions: - - {description: Larch is a open-source library and set of applications for processing - and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray - fluorescence and diffraction image data from synchrotron beamlines., markedDefault: false, - versionName: 0.9.80_py312} - categories: chemistry, quantum chemistry defaultVersionName: '4.1' description: CP2K is a quantum chemistry and solid state physics software package @@ -5790,6 +5779,31 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: '4.1' + - categories: chemistry, quantum chemistry + defaultVersionName: 5.0.3 + description: ORCA is a flexible, efficient and easy-to-use general purpose tool + for quantum chemistry. + package: orca + url: https://orcaforum.kofo.mpg.de/ + versions: + - description: ORCA is a flexible, efficient and easy-to-use general purpose + tool for quantum chemistry. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 4.2.1 + - description: ORCA is a flexible, efficient and easy-to-use general purpose + tool for quantum chemistry. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 5.0.0 + - description: ORCA is a flexible, efficient and easy-to-use general purpose + tool for quantum chemistry. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 5.0.3 - categories: chemistry, molecular dynamics defaultVersionName: '2023.1' description: GROMACS is a versatile package to perform molecular dynamics, i.e. @@ -5873,31 +5887,50 @@ software_modules: versions: - {description: A C++ toolkit for working with macromolecular coordinate files., markedDefault: false, versionName: 2.0.20} - - categories: chemistry, quantum chemistry - defaultVersionName: 5.0.3 - description: ORCA is a flexible, efficient and easy-to-use general purpose tool - for quantum chemistry. - package: orca - url: https://orcaforum.kofo.mpg.de/ + - categories: chemistry, computational chemistry + defaultVersionName: 5.4.1 + description: The Vienna Ab initio Simulation Package (VASP) is a computer program + for atomic scale materials modelling, e.g. electronic structure calculations + and quantum-mechanical molecular dynamics, from first principles. + package: vasp + url: https://www.vasp.at versions: - - description: ORCA is a flexible, efficient and easy-to-use general purpose - tool for quantum chemistry. + - description: The Vienna Ab initio Simulation Package (VASP) is a computer + program for atomic scale materials modelling, e.g. electronic structure + calculations and quantum-mechanical molecular dynamics, from first principles. markedDefault: false properties: + arch: {gpu: 1} + license: {restricted: 1} parallel: {mpi: 1} - versionName: 4.2.1 - - description: ORCA is a flexible, efficient and easy-to-use general purpose - tool for quantum chemistry. + versionName: 6.1.1 + - description: The Vienna Ab initio Simulation Package (VASP) is a computer + program for atomic scale materials modelling, e.g. electronic structure + calculations and quantum-mechanical molecular dynamics, from first principles. markedDefault: false properties: + arch: {gpu: 1} + license: {restricted: 1} parallel: {mpi: 1} - versionName: 5.0.0 - - description: ORCA is a flexible, efficient and easy-to-use general purpose - tool for quantum chemistry. + versionName: 6.3.2 + - description: The Vienna Ab initio Simulation Package (VASP) is a computer + program for atomic scale materials modelling, e.g. electronic structure + calculations and quantum-mechanical molecular dynamics, from first principles. markedDefault: false properties: + arch: {gpu: 1} + license: {restricted: 1} parallel: {mpi: 1} - versionName: 5.0.3 + versionName: 6.4.1 + - description: The Vienna Ab initio Simulation Package (VASP) is a computer + program for atomic scale materials modelling, e.g. electronic structure + calculations and quantum-mechanical molecular dynamics, from first principles. + markedDefault: true + properties: + arch: {gpu: 1} + license: {restricted: 1} + parallel: {mpi: 1} + versionName: 5.4.1 - categories: chemistry, quantum chemistry defaultVersionName: '7.1' description: Quantum ESPRESSO is an integrated suite of Open-Source computer @@ -5996,6 +6029,14 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: '20230802' + - categories: chemistry, crystallography + defaultVersionName: '1.4' + description: A macromolecular superposition library. + package: ssm + url: https://www.ccp4.ac.uk/ + versions: + - {description: A macromolecular superposition library., markedDefault: false, + versionName: '1.4'} - categories: chemistry, crystallography defaultVersionName: 3.4.4 description: VESTA is a 3D visualization program for structural models, volumetric @@ -6006,47 +6047,19 @@ software_modules: - {description: 'VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.', markedDefault: false, versionName: 3.4.4} - - categories: chemistry, crystallography - defaultVersionName: '1.4' - description: A macromolecular superposition library. - package: ssm - url: https://www.ccp4.ac.uk/ - versions: - - {description: A macromolecular superposition library., markedDefault: false, - versionName: '1.4'} - - categories: chemistry, quantum chemistry - defaultVersionName: '7.1' - description: Quantum ESPRESSO is an integrated suite of Open-Source computer - codes for electronic-structure calculations and materials modeling at the - nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. - package: quantum-espresso_gpu - url: https://www.quantum-espresso.org + - categories: chemistry, cheminformatics + defaultVersionName: 2018.09.1_py27 + description: RDKit is a collection of cheminformatics and machine-learning software + written in C++ and Python. + package: py-rdkit + url: http://www.rdkit.org versions: - - description: GPU-accelerated Quantum ESPRESSO using CUDA FORTRAN - family: qe - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '1.1' - - description: Quantum ESPRESSO is an integrated suite of Open-Source computer - codes for electronic-structure calculations and materials modeling at the - nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. - family: qe - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '7.0' - - description: Quantum ESPRESSO is an integrated suite of Open-Source computer - codes for electronic-structure calculations and materials modeling at the - nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. - family: qe - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '7.1' + - {description: RDKit is a collection of cheminformatics and machine-learning + software written in C++ and Python., markedDefault: false, versionName: 2018.09.1_py36} + - {description: RDKit is a collection of cheminformatics and machine-learning + software written in C++ and Python., markedDefault: false, versionName: 2022.09.1_py39} + - {description: RDKit is a collection of cheminformatics and machine-learning + software written in C++ and Python., markedDefault: true, versionName: 2018.09.1_py27} - categories: chemistry, molecular dynamics defaultVersionName: '20220426' description: The QUIP package is a collection of software tools to carry out diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml index f00520499..3621cef17 100644 --- a/src/docs/software/updates.xml +++ b/src/docs/software/updates.xml @@ -5,6 +5,15 @@ Sherlock software update feed https://www.sherlock.stanford.edu/docs/software/list + + New module: chemistry/mosaics version 1.0.0 + A collection of tools for characterizing membrane structure and dynamics within simulated trajectories of molecular systems. + https://github.com/MOSAICS-NIH/MOSAICS + https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.0.0#mosaics + chemistry, molecular dynamics + kilian@stanford.edu (Kilian Cavalotti) + Mon, 26 Aug 2024 15:24:34 -0700 + New module: devel/py-regex version .base @@ -149,149 +158,5 @@ kilian@stanford.edu (Kilian Cavalotti) Tue, 9 Jul 2024 14:29:24 -0700 - - New module: biology/longshot version 1.0.0 - Longshot is a variant calling tool for diploid genomes using long error prone reads. - https://github.com/pjedge/longshot - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.0.0#longshot - biology, genomics - kilian@stanford.edu (Kilian Cavalotti) - Wed, 29 May 2024 09:16:34 -0700 - - - New version: biology/dorado version 0.7.0 - - - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.7.0#dorado - - kilian@stanford.edu (Kilian Cavalotti) - Fri, 24 May 2024 10:51:36 -0700 - - - New version: system/gh version 1.9.1 - - - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.9.1#gh - - kilian@stanford.edu (Kilian Cavalotti) - Mon, 20 May 2024 13:35:10 -0700 - - - New version: system/gh version 2.49.2 - gh is GitHub on the command line. It brings pull requests, issues, and other GitHub concepts to the terminal next to where you are already working with git and your code. - https://cli.github.com/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=2.49.2#gh - system, scm - kilian@stanford.edu (Kilian Cavalotti) - Mon, 20 May 2024 13:35:10 -0700 - - - New version: system/git version 2.39.1 - - - https://www.sherlock.stanford.edu/docs/software/list/?add:v=2.39.1#git - - kilian@stanford.edu (Kilian Cavalotti) - Mon, 20 May 2024 13:25:10 -0700 - - - New version: system/git version 2.45.1 - Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. - http://git-scm.com - https://www.sherlock.stanford.edu/docs/software/list/?add:v=2.45.1#git - system, scm - kilian@stanford.edu (Kilian Cavalotti) - Mon, 20 May 2024 13:25:10 -0700 - - - New module: system/webkitgtk version 2.28.4 - WebKitGTK is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers. - https://webkitgtk.org/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=2.28.4#webkitgtk - system, libs - kilian@stanford.edu (Kilian Cavalotti) - Fri, 17 May 2024 13:47:26 -0700 - - - New module: system/unifdef version 2.12 - The unifdef utility selectively processes conditional C preprocessor #if and #ifdef directives. - https://dotat.at/prog/unifdef/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=2.12#unifdef - system, tool - kilian@stanford.edu (Kilian Cavalotti) - Fri, 17 May 2024 13:47:16 -0700 - - - New module: biology/cellranger-atac version 2.1.0 - Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data. - https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac - https://www.sherlock.stanford.edu/docs/software/list/?add:v=2.1.0#cellranger-atac - biology, genomics - kilian@stanford.edu (Kilian Cavalotti) - Fri, 17 May 2024 10:07:43 -0700 - - - New version: math/py-tensorrt version 10.0.1_py312 - Python bindings for the TensorRT library. - https://developer.nvidia.com/tensorrt - https://www.sherlock.stanford.edu/docs/software/list/?add:v=10.0.1_py312#py-tensorrt - math, deep learning - kilian@stanford.edu (Kilian Cavalotti) - Wed, 15 May 2024 14:59:26 -0700 - - - New version: math/tensorrt version 10.0.1.6 - NVIDIA TensorRT™ is a high-performance deep learning inference optimizer and runtime that delivers low latency, high-throughput inference for deep learning applications. - https://developer.nvidia.com/tensorrt - https://www.sherlock.stanford.edu/docs/software/list/?add:v=10.0.1.6#tensorrt - math, deep learning - kilian@stanford.edu (Kilian Cavalotti) - Wed, 15 May 2024 14:59:13 -0700 - - - New module: physics/py-gdal-utils version 3.4.1_py39 - gdal-utils is the GDAL Python Utilities distribution. - https://pypi.org/project/gdal-utils/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=3.4.1_py39#py-gdal-utils - physics, geoscience - kilian@stanford.edu (Kilian Cavalotti) - Tue, 14 May 2024 11:36:58 -0700 - - - New module: system/py-nvitop version .base - - - https://www.sherlock.stanford.edu/docs/software/list/?add:v=.base#py-nvitop - - kilian@stanford.edu (Kilian Cavalotti) - Tue, 7 May 2024 14:09:40 -0700 - - - New module: system/py-nvitop version 1.3.2_py312 - An interactive NVIDIA-GPU process viewer and beyond. - https://github.com/XuehaiPan/nvitop - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.3.2_py312#py-nvitop - system, resource monitoring - kilian@stanford.edu (Kilian Cavalotti) - Tue, 7 May 2024 14:09:40 -0700 - - - New module: system/py-nvitop version 1.3.2_py39 - An interactive NVIDIA-GPU process viewer and beyond. - https://github.com/XuehaiPan/nvitop - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.3.2_py39#py-nvitop - system, resource monitoring - kilian@stanford.edu (Kilian Cavalotti) - Tue, 7 May 2024 14:09:40 -0700 - - - New module: system/py-nvitop version default - An interactive NVIDIA-GPU process viewer and beyond. - https://github.com/XuehaiPan/nvitop - https://www.sherlock.stanford.edu/docs/software/list/?add:v=default#py-nvitop - system, resource monitoring - kilian@stanford.edu (Kilian Cavalotti) - Tue, 7 May 2024 14:09:40 -0700 -