From e63790745bc3d0ba975af7aa1d79f5254a3b420b Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Wed, 6 Mar 2024 14:18:08 -0800 Subject: [PATCH] docs: updated software list --- includes/data/software.yml | 22 ++++++++++++++++- src/docs/software/updates.xml | 45 ++++++++++++++--------------------- 2 files changed, 39 insertions(+), 28 deletions(-) diff --git a/includes/data/software.yml b/includes/data/software.yml index 2e6055401..2cfa4fc38 100644 --- a/includes/data/software.yml +++ b/includes/data/software.yml @@ -2302,6 +2302,9 @@ software_modules: - {description: The SciPy library provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization., family: scipy, markedDefault: false, versionName: 1.10.1_py39} + - {description: The SciPy library provides many user-friendly and efficient + numerical routines such as routines for numerical integration and optimization., + family: scipy, markedDefault: false, versionName: 1.12.0_py312} - {description: The SciPy library provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization., family: scipy, markedDefault: true, versionName: 1.1.0_py27} @@ -3710,6 +3713,12 @@ software_modules: properties: arch: {gpu: 1} versionName: 4.7.0 + - description: OpenCV (Open Source Computer Vision Library) is an open source + computer vision and machine learning software library. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 4.9.0 - description: OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. markedDefault: true @@ -5155,7 +5164,7 @@ software_modules: - {description: A Python framework for the analysis and visualization of trees., markedDefault: false, versionName: 3.0.0_py27} - categories: biology, genomics - defaultVersionName: 0.12.0 + defaultVersionName: 1.10.0 description: Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments. package: salmon @@ -5164,6 +5173,9 @@ software_modules: - {description: Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments., markedDefault: false, versionName: 0.12.0} + - {description: Highly-accurate & wicked fast transcript-level quantification + from RNA-seq reads using lightweight alignments., markedDefault: false, + versionName: 1.10.0} - categories: biology, genomics defaultVersionName: 1.1.3_py27 description: Fit-Hi-C is a tool for assigning statistical confidence estimates @@ -7097,6 +7109,14 @@ software_modules: properties: arch: {gpu: 1} versionName: 12.2.0 + - description: CUDA is a parallel computing platform and application programming + interface (API) model created by Nvidia. It allows software developers and + software engineers to use a CUDA-enabled graphics processing unit (GPU) + for general purpose processing. + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 12.4.0 - description: CUDA is a parallel computing platform and application programming interface (API) model created by Nvidia. It allows software developers and software engineers to use a CUDA-enabled graphics processing unit (GPU) diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml index c5546a045..de3debadf 100644 --- a/src/docs/software/updates.xml +++ b/src/docs/software/updates.xml @@ -5,6 +5,24 @@ Sherlock software update feed https://www.sherlock.stanford.edu/docs/software/list + + New version: biology/salmon version 1.10.0 + Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments. + https://combine-lab.github.io/salmon + https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.10.0#salmon + biology, genomics + kilian@stanford.edu (Kilian Cavalotti) + Wed, 6 Mar 2024 14:17:16 -0800 + + + New version: devel/cuda version 12.4.0 + CUDA is a parallel computing platform and application programming interface (API) model created by Nvidia. It allows software developers and software engineers to use a CUDA-enabled graphics processing unit (GPU) for general purpose processing. + https://developer.nvidia.com/cuda-toolkit + https://www.sherlock.stanford.edu/docs/software/list/?add:v=12.4.0#cuda + devel, language + kilian@stanford.edu (Kilian Cavalotti) + Tue, 5 Mar 2024 14:39:10 -0800 + New version: viz/py-plotly version 5.19.0_py312 Plotly's Python graphing library makes interactive, publication-quality graphs online. @@ -203,32 +221,5 @@ kilian@stanford.edu (Kilian Cavalotti) Mon, 8 Jan 2024 14:23:50 -0800 - - New version: physics/geos version 3.12.1 - GEOS is a C/C++ library for computational geometry with a focus on algorithms used in geographic information systems (GIS) software. - https://libgeos.org - https://www.sherlock.stanford.edu/docs/software/list/?add:v=3.12.1#geos - physics, geoscience - kilian@stanford.edu (Kilian Cavalotti) - Tue, 12 Dec 2023 11:17:10 -0800 - - - New version: biology/kallisto version 0.50.1 - kallisto is a program for quantifying abundances of transcripts from RNA-Seq data using high-throughput sequencing reads. - https://pachterlab.github.io/kallisto/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.50.1#kallisto - biology, genomics - kilian@stanford.edu (Kilian Cavalotti) - Wed, 29 Nov 2023 13:50:00 -0800 - - - New version: system/py-matlab-proxy version 0.10.0_py39 - matlab-proxy is a Python package which enables you to launch MATLAB and access it from a web browser. - https://github.com/mathworks/matlab-proxy - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.10.0_py39#py-matlab-proxy - system, tools - kilian@stanford.edu (Kilian Cavalotti) - Wed, 29 Nov 2023 10:37:32 -0800 -