diff --git a/includes/data/software.yml b/includes/data/software.yml index d71220993..f83783701 100644 --- a/includes/data/software.yml +++ b/includes/data/software.yml @@ -853,12 +853,10 @@ software_modules: versions: - {description: 'LibreSSL is a version of the TLS/crypto stack forked from OpenSSL in 2014, with goals of modernizing the codebase, improving security, and - applying best practice development processes.', family: ssl, markedDefault: false, - versionName: 2.5.3} + applying best practice development processes.', markedDefault: false, versionName: 2.5.3} - {description: 'LibreSSL is a version of the TLS/crypto stack forked from OpenSSL in 2014, with goals of modernizing the codebase, improving security, and - applying best practice development processes.', family: ssl, markedDefault: false, - versionName: 3.2.1} + applying best practice development processes.', markedDefault: false, versionName: 3.2.1} - categories: system, file management defaultVersionName: 0.9.3 description: fpart sorts files and packs them into partitions. @@ -1909,7 +1907,7 @@ software_modules: url: https://www.openssl.org/ versions: - {description: OpenSSL is a full-featured toolkit for general-purpose cryptography - and secure communication., family: ssl, markedDefault: false, versionName: 3.0.7} + and secure communication., markedDefault: false, versionName: 3.0.7} - categories: system, libs defaultVersionName: 1.8.2 description: Libgcrypt is a general purpose cryptographic library originally @@ -4379,13 +4377,13 @@ software_modules: - {description: Python API for comprehensive GWAS analysis using GEMMA., markedDefault: false, versionName: 0.8.9_py39} - categories: biology, cryo-em - defaultVersionName: '2.1' + defaultVersionName: 4.0.1 description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). package: relion - url: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page + url: https://github.com/3dem/relion versions: - description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach @@ -4405,6 +4403,15 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: '2.1' + - description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) + is a stand-alone computer program that employs an empirical Bayesian approach + to refinement of (multiple) 3D reconstructions or 2D class averages in electron + cryo-microscopy (cryo-EM). + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: 4.0.1 - categories: biology, genomics defaultVersionName: 2.10.0 description: 'HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.' diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml index facde660e..35adcff35 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 version: biology/relion version 4.0.1 + RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). + https://github.com/3dem/relion + https://www.sherlock.stanford.edu/docs/software/list/?add:v=4.0.1#relion + biology, cryo-em + kilian@stanford.edu (Kilian Cavalotti) + Tue, 24 Oct 2023 16:24:43 -0700 + New module: devel/code-server version 4.16.1 Run VS Code on any machine anywhere and access it in the browser. @@ -194,41 +203,5 @@ kilian@stanford.edu (Kilian Cavalotti) Fri, 18 Aug 2023 13:56:51 -0700 - - New module: system/jansson version 2.13.1 - C library for encoding, decoding and manipulating JSON data. - https://github.com/akheron/jansson - https://www.sherlock.stanford.edu/docs/software/list/?add:v=2.13.1#jansson - system, libs - kilian@stanford.edu (Kilian Cavalotti) - Mon, 14 Aug 2023 08:29:17 -0700 - - - New module: physics/swash version 9.01a - SWASH (an acronym of Simulating WAves till SHore) is a non-hydrostatic wave-flow model. - https://swash.sourceforge.io/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=9.01a#swash - physics, geoscience - kilian@stanford.edu (Kilian Cavalotti) - Thu, 20 Jul 2023 17:09:20 -0700 - - - New module: biology/py-vcf2gwas version 0.8.9_py39 - Python API for comprehensive GWAS analysis using GEMMA. - https://github.com/frankvogt/vcf2gwas - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.8.9_py39#py-vcf2gwas - biology, genomics - kilian@stanford.edu (Kilian Cavalotti) - Mon, 17 Jul 2023 18:23:53 -0700 - - - New module: biology/gemma version 0.98.5 - GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. - https://github.com/genetics-statistics/GEMMA - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.98.5#gemma - biology, genomics - kilian@stanford.edu (Kilian Cavalotti) - Mon, 17 Jul 2023 18:23:37 -0700 -