From f45e51e8b3a930a6c83f39ccffc9438dbf64b949 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 1 Jan 2024 05:27:06 +0000 Subject: [PATCH] Add changes --- _data/containers.yaml | 8 +- _data/repos.yml | 544 +- .../repeatexplorer/repex_tarean/Singularity | 36 + .../repex_tarean/Singularity.0.3.7.5996768 | 38 + .../repex_tarean/Singularity.0.3.8.dbaa07f | 38 + assets/js/repos.js | 34605 ++++++++-------- 6 files changed, 17705 insertions(+), 17564 deletions(-) create mode 100644 _recipes/repeatexplorer/repex_tarean/Singularity create mode 100644 _recipes/repeatexplorer/repex_tarean/Singularity.0.3.7.5996768 create mode 100644 _recipes/repeatexplorer/repex_tarean/Singularity.0.3.8.dbaa07f diff --git a/_data/containers.yaml b/_data/containers.yaml index 2b29113f..f51aab50 100644 --- a/_data/containers.yaml +++ b/_data/containers.yaml @@ -1,5 +1,5 @@ bases: -- count: 1928 +- count: 1931 name: ubuntu - count: 430 name: nvidia/cuda @@ -1974,7 +1974,7 @@ bases: - count: 1 name: nitesh1989/biocparallel-example bootstraps: -- count: 6273 +- count: 6276 name: docker - count: 472 name: shub @@ -2909,7 +2909,7 @@ orgs: name: nitesh1989 tags: latest: 683 - other: 5825 + other: 5828 versions: /nrs/funke/singularity/linajea/pylp_base: v1.5.img: 1 @@ -5481,7 +5481,7 @@ versions: '18.10': 9 '19.04': 33 '19.10': 16 - '20.04': 426 + '20.04': 429 '20.04 ': 1 '20.10': 3 '21.04': 3 diff --git a/_data/repos.yml b/_data/repos.yml index d1cbd75e..bc94953b 100644 --- a/_data/repos.yml +++ b/_data/repos.yml @@ -2814,10 +2814,10 @@ APSIMInitiative/APSIMClassic: rel="nofollow">Here.
' - stargazers_count: 26 + stargazers_count: 27 subscribers_count: 16 topics: [] - updated_at: 1689914576.0 + updated_at: 1703281675.0 ARCLeeds/christmas-devcontainers-talk: data_format: 2 description: christmas-devcontainers-talk @@ -5668,18 +5668,18 @@ AuReMe/metage2metabo: full_name: AuReMe/metage2metabo latest_release: 1.5.4 readme: "\nPlease have a look at the notebook Introduction.ipynb, or try it directly here: (requires Google account)
@@ -15690,46 +15690,46 @@ DeepLearnPhysics/larcv2-singularity: data_format: 2 description: null filenames: - - arxiv/Singularity.ubuntu16.04-gpu-larcv_develop - - arxiv/Singularity.ub16.04-tf1.10.1-torch0.4.1 - - arxiv/Singularity.ubuntu16.04-gpu - - arxiv/Singularity.ubuntu16.04-larcv_develop - - arxiv/Singularity.ub16.04-tf1.11.0-torch0.4.1 - - arxiv/Singularity.ub16.04-tf1.11.0-torch0.4.1-root6.14.04 - - arxiv/Singularity.ub16.04-tf1.7-torch0.4 - - arxiv/Singularity.ub16.04-tf1.10.1-torch0.4.1-root6.14.04 - - arxiv/Singularity.ubuntu16.04-gpu-py3 - - arxiv/Singularity.ubuntu16.04-basic - - recipes/Singularity.ub16.04-cuda90-pytorch1.0.0-scn - - recipes/Singularity - - recipes/Singularity.ub18.04-gpu-ana0 - - recipes/Singularity.ub18.04-cuda100-py3-pytorch1.1.0-scn-docker - - recipes/Singularity.ub18.04-gpu-ana0-mn - - recipes/Singularity.ub16.04-cuda90-pytorchdev20181015 - - recipes/Singularity.ub18.04-cpu-ana0 + - recipes/Singularity.ub18.04-cuda100-py3-pytorch1.0.1-scn + - recipes/Singularity.ub18.04-gpu-ana0-ml-larcv2 + - recipes/Singularity.ub16.04-cuda100-pytorch1.0.0-scn + - recipes/Singularity.ub18.04-gpu - recipes/Singularity.ub18.04-cuda10.1-ml-larcv2 - - recipes/Singularity.ub16.04-cuda90-tf1.12.0 - - recipes/Singularity.ub16.04-cuda90-pytorch0.4.1 + - recipes/Singularity.ub18.04-cuda100-py3-pytorch1.1.0-scn + - recipes/Singularity.ub16.04-cuda90-pytorchdev20181015 + - recipes/Singularity.ub18.04-gpu-ana0 - recipes/Singularity.ub18.04-cpu - recipes/Singularity.ub16.04-cuda100-pytorchdev20181215 - - recipes/Singularity.ub18.04-gpu + - recipes/Singularity.HKMLWorkshop + - recipes/Singularity.ub18.04-gpu-ana0-mn + - recipes/Singularity.ub18.04-cpu-ana0 - recipes/Singularity.ub16.04-cuda90-py3-pytorch1.0.1-scn - - recipes/Singularity.ub16.04-cuda100-pytorch1.0.0-scn - - recipes/Singularity.ub18.04-cuda100-py3-pytorch1.1.0-scn - - recipes/Singularity.ub18.04-gpu-ana0-ml-larcv2 - recipes/Singularity.ub18.04-cuda10.2-extra - - recipes/Singularity.ub18.04-cuda100-py3-pytorch1.0.1-scn - - recipes/Singularity.ub18.04-cpu-ana0-larcv2 - - recipes/Singularity.HKMLWorkshop + - recipes/Singularity - recipes/Singularity.ub18.04-gpu-ana0-ml + - recipes/Singularity.ub18.04-cpu-ana0-larcv2 + - recipes/Singularity.ub16.04-cuda90-tf1.12.0 + - recipes/Singularity.ub18.04-cuda100-py3-pytorch1.1.0-scn-docker + - recipes/Singularity.ub16.04-cuda90-pytorch1.0.0-scn + - recipes/Singularity.ub16.04-cuda90-pytorch0.4.1 + - arxiv/Singularity.ubuntu16.04-larcv_develop + - arxiv/Singularity.ub16.04-tf1.10.1-torch0.4.1 + - arxiv/Singularity.ub16.04-tf1.10.1-torch0.4.1-root6.14.04 + - arxiv/Singularity.ub16.04-tf1.11.0-torch0.4.1 + - arxiv/Singularity.ubuntu16.04-gpu + - arxiv/Singularity.ub16.04-tf1.7-torch0.4 + - arxiv/Singularity.ubuntu16.04-basic + - arxiv/Singularity.ub16.04-tf1.11.0-torch0.4.1-root6.14.04 + - arxiv/Singularity.ubuntu16.04-gpu-larcv_develop + - arxiv/Singularity.ubuntu16.04-gpu-py3 full_name: DeepLearnPhysics/larcv2-singularity latest_release: null readme: ' @@ -17509,13 +17509,13 @@ EI-CoreBioinformatics/mikado: full_name: EI-CoreBioinformatics/mikado latest_release: v2.3.4 readme: "\nTo install MRChem in a Conda environment\
\ myenv
:
$ conda create -n myenv\n$ conda activate\
@@ -39106,8 +39106,8 @@ MRChemSoft/mrchem:
Note that the MPI image requires that a compatible MPI library is installed\
\ and\navailable on the host. For information on how to launch the container:
\n\
$ singularity run-help mrchem-mpi.sif\n
\n"
- stargazers_count: 23
- subscribers_count: 8
+ stargazers_count: 24
+ subscribers_count: 9
topics:
- multiwavelets
- computational-chemistry
@@ -39116,7 +39116,7 @@ MRChemSoft/mrchem:
- c-plus-plus
- python
- density-functional-theory
- updated_at: 1700223726.0
+ updated_at: 1703731199.0
MRChemSoft/mrchem-singularity:
data_format: 2
description: Hosting recipes for Singularity Hub
@@ -39129,7 +39129,7 @@ MRChemSoft/mrchem-singularity:
full_name: MRChemSoft/mrchem-singularity
latest_release: null
readme: "\n
\n"
stargazers_count: 1
- subscribers_count: 6
+ subscribers_count: 7
topics: []
updated_at: 1641394651.0
MRIresearch/NeuroPipelines:
@@ -39335,7 +39335,7 @@ MRtrix3/mrtrix3:
\ octicon-link\">MRtrix\n\nMRtrix3 can be installed /\ \ run through multiple avenues:
\n\n\n" - stargazers_count: 13 + stargazers_count: 14 subscribers_count: 2 topics: - collision-avoidance - gazebo-simulator - robot-navigation - updated_at: 1702557024.0 + updated_at: 1703474135.0 TheJacksonLaboratory/acm-bcb-singularity2021: data_format: 2 description: Singularity Course Repo for 2021 ACM-BCB Conference @@ -60107,16 +60107,16 @@ UPennBJPrager/CNT_Research_Template: \ aria-hidden=\"true\" tabindex=\"-1\" href=\"#cnt-research-repository-template\"\ >CNT Research\ \ Repository Template
The purpose of this template is to consolidate\ \ shared libraries and enable consistent workflows and tests for most projects\ @@ -60524,16 +60524,16 @@ VALENCE-software/VALENCE: full_name: VALENCE-software/VALENCE latest_release: v1.0 readme: "
\nStatus for Development Branch:\n\n
\nNote: if looking for content\
\ of geoclaw-landspill-cases
, please checkout tag\nv0.1
.\
@@ -75034,7 +75034,7 @@ bbodi/rustarok:
>Thanks\n\n
\n"
- stargazers_count: 263
+ stargazers_count: 265
subscribers_count: 15
topics:
- rust
@@ -75045,7 +75045,7 @@ bbodi/rustarok:
- multiplayer
- 2d
- 3d
- updated_at: 1702409847.0
+ updated_at: 1703043777.0
bcgsc/orca:
data_format: 2
description: ':whale: Genomics Research Container Architecture'
@@ -76907,8 +76907,8 @@ biocorecrg/C4LWG-2018:
description: Hands-on tutorial on Nextflow and Containers (Docker and Singularity).
Paris 2018.
filenames:
- - Singularity
- Singularity.xenial
+ - Singularity
full_name: biocorecrg/C4LWG-2018
latest_release: null
readme: "
-
-
The singularity container has been built through singularity hub.
- @@ -78594,15 +78594,15 @@ bioexcel/zip_container: - Singularity.latest full_name: bioexcel/zip_container latest_release: null - readme: ' @@ -78709,8 +78709,8 @@ bioexcel/zip_container:The singularity container has been built through singularity hub.
- @@ -84925,7 +84925,7 @@ connor-lab/singularity-recipes:./build_containers.sh
@@ -90587,8 +90587,8 @@ datalad/datalad-neuroimaging:
data_format: 2
description: DataLad extension for neuroimaging research
filenames:
- - tools/Singularity
- tools/Singularity.devmaster
+ - tools/Singularity
full_name: datalad/datalad-neuroimaging
latest_release: 0.3.4
readme: " ____ _ _ _\n| _ \\ __\
@@ -90596,32 +90596,32 @@ datalad/datalad-neuroimaging:
\ | / _` |\n| |_| || (_| || |_ | (_| || |___ | (_| || (_| |\n|____/ \\__,_| \\\
__| \\__,_||_____| \\__,_| \\__,_|\n Neuroimaging\n\
\n\nThis extension enhances DataLad (http://datalad.org) for working\ @@ -94286,11 +94286,11 @@ diplomacy/research: data_format: 2 description: Supervised and RL Models for No Press Diplomacy filenames: - - diplomacy_research/containers/ubuntu-cuda10/Singularity - - diplomacy_research/containers/redis/Singularity + - diplomacy_research/containers/research/Singularity - diplomacy_research/containers/albert-ai/Singularity + - diplomacy_research/containers/redis/Singularity + - diplomacy_research/containers/ubuntu-cuda10/Singularity - diplomacy_research/containers/tensorflow-serving/Singularity - - diplomacy_research/containers/research/Singularity full_name: diplomacy/research latest_release: v1.0.0 readme: "
This README file provides some essential\ \ information to install/use PanACoTA. But it is better to read the NAR Genomics and Bioinformatics, Volume 3, Issue\ \ 1, March 2021\n
\nContent of this README:
\n\Installation
\nA very simple way to install the last\ \ stable version. This will install files in your python site-packages folder.
\n\ @@ -105794,10 +105794,10 @@ gem-pasteur/PanACoTA: true\" tabindex=\"-1\" href=\"#-from-conda\">Be careful while using conda, especially\ \ if you are not familiar with it. We advise to install PanACoTA in a dedicated\ @@ -105816,7 +105816,7 @@ gem-pasteur/PanACoTA: >From zip\ \ version\n
For people wanting to download source code of a specific version,\ \ we provide releases. You can download last one here:
\nmake html\n
\nThen, open doc/build/html/index.html
\
\ on your browser.
The online version will be automatically updated when\ \ pushed on master branch.
\n" - stargazers_count: 61 + stargazers_count: 62 subscribers_count: 6 topics: [] - updated_at: 1701096927.0 + updated_at: 1702998820.0 genepattern/nmf-gpu: data_format: 2 description: GPU-optimized NMF and variations @@ -107859,14 +107859,14 @@ github-linguist/linguist: \ by their repositories' respective licenses.\nvendor/README.md
\
\ lists the repository for each grammar.\nAll other files are covered by\
\ the MIT license, see LICENSE
.
TraitRELAX is an open-source software\ @@ -121540,7 +121540,7 @@ jlboat/BioinfoContainers:
Various Singularity recipes I''ve used to generate bioinformatics containers
@@ -122321,7 +122321,7 @@ jolars/HessianScreening: aria-hidden="true" class="octicon octicon-link">Code for the Hessian Screening Rule - @@ -124517,7 +124517,7 @@ kalibera/rchk: @@ -126571,28 +126571,28 @@ kipoi/kipoi: \ aria-hidden=\"true\" tabindex=\"-1\" href=\"#kipoi-model-zoo-for-genomics\"\ >Kipoi: Model\ \ zoo for genomics\n\n\t\n\t\n\n\n\t\n\t\n\n\n\t\n\t\n\n\n\t\n\t\n\n\n\t\n\t\n\n\n\t\n\t\n\nThis repository implements a python package and\ \ a command-line interface (CLI) to access and use models from Kipoi-compatible\ \ model zoo's.
\n\nKipoi is MIT-style licensed, as found\ \ in the LICENSE file.
\n" - stargazers_count: 226 + stargazers_count: 229 subscribers_count: 22 topics: [] - updated_at: 1700854336.0 + updated_at: 1703906053.0 kipoi/models: data_format: 2 description: Model zoo for genomics @@ -129992,18 +129992,18 @@ litebird/litebird_sim: full_name: litebird/litebird_sim latest_release: v0.10.0 readme: "\n\n\n\n\n\n \n singularity-pytorch-gpu
@@ -137980,7 +137980,7 @@ ml4ai/UA-hpc-containers: Container Repository @@ -138011,13 +138011,13 @@ ml4ai/automates: >Automated\ \ Model Assembly\n \n \n \n \n \n \n \n \n \n \n
\nThis repository holds the source code\ \ for the AutoMATES documentation\nand several component pipelines.
\nFor\ @@ -138064,36 +138064,37 @@ mlcommons/mlcube_examples: - mnist/Singularity.recipe full_name: mlcommons/mlcube_examples latest_release: null - readme: "
The machine learning (ML) community has seen an explosive\ - \ growth and innovation in the last decade. New models emerge\non a daily basis,\ - \ but sharing those models remains an ad-hoc process. Often, when a researcher\ - \ wants to use a model\nproduced elsewhere, they must waste hours or days on a\ - \ frustrating attempt to get the model to work. Similarly, a ML\nengineer may\ - \ struggle to port and tune models between development and production environments\ - \ which can be significantly\ndifferent from each other. This challenge is magnified\ - \ when working with a set of models, such as reproducing related\nwork, employing\ - \ a performance benchmark suite like MLPerf, or developing model management infrastructures.\n\ - Reproducibility, transparency and consistent performance measurement are cornerstones\ - \ of good science and engineering.
\nThe field needs to make sharing models\ - \ simple for model creators, model users, developers and operators for both\n\ - experimental and production purpose while following responsible practices. Prior\ - \ works in the MLOps space have provided\na variety of tools and processes that\ - \ simplify user journey of deploying and managing ML in various environments,\n\ - which include management of models, datasets, and dependencies, tracking of metadata\ - \ and experiments, deployment and\nmanagement of ML lifecycles, automation of\ - \ performance evaluations and analysis, etc.
\nWe propose an MLCube\xAE\ - , a contract for packaging ML tasks and models that enables easy sharing and consistent\ - \ reproduction\nof models, experiments and benchmarks amidst these existing MLOps\ - \ processes. MLCube differs from an operation tool by\nacting as a contract and\ - \ specification as opposed to a product or implementation.
\nThis repository\ - \ contains a number of MLCube examples that can run in different environments\ - \ using\nMLCube runners.
\n\ -The machine learning\ + \ (ML) community has seen an explosive growth and innovation in the last decade.\ + \ New models emerge\non a daily basis, but sharing those models remains an ad-hoc\ + \ process. Often, when a researcher wants to use a model\nproduced elsewhere,\ + \ they must waste hours or days on a frustrating attempt to get the model to work.\ + \ Similarly, a ML\nengineer may struggle to port and tune models between development\ + \ and production environments which can be significantly\ndifferent from each\ + \ other. This challenge is magnified when working with a set of models, such as\ + \ reproducing related\nwork, employing a performance benchmark suite like MLPerf,\ + \ or developing model management infrastructures.\nReproducibility, transparency\ + \ and consistent performance measurement are cornerstones of good science and\ + \ engineering.
\nThe field needs to make sharing models simple for model\ + \ creators, model users, developers and operators for both\nexperimental and production\ + \ purpose while following responsible practices. Prior works in the MLOps space\ + \ have provided\na variety of tools and processes that simplify user journey of\ + \ deploying and managing ML in various environments,\nwhich include management\ + \ of models, datasets, and dependencies, tracking of metadata and experiments,\ + \ deployment and\nmanagement of ML lifecycles, automation of performance evaluations\ + \ and analysis, etc.
\nWe propose an MLCube\xAE, a contract for packaging\ + \ ML tasks and models that enables easy sharing and consistent reproduction\n\ + of models, experiments and benchmarks amidst these existing MLOps processes. MLCube\ + \ differs from an operation tool by\nacting as a contract and specification as\ + \ opposed to a product or implementation.
\nThis repository contains a number\ + \ of MLCube examples that can run in different environments using\nMLCube runners.
\nNot all files are written by humans.\ \ Generated will detect files that have been\ngenerated by computers. Items like\ @@ -149958,13 +149959,13 @@ openhackathons-org/gpubootcamp: full_name: openhackathons-org/gpubootcamp latest_release: null readme: '
@@ -150007,7 +150008,7 @@ openhackathons-org/gpubootcamp: rel="nofollow">OpenACC Slack Channel. ' - stargazers_count: 479 + stargazers_count: 481 subscribers_count: 21 topics: - machine-learning @@ -150022,7 +150023,7 @@ openhackathons-org/gpubootcamp: - rapidsai - openmp - ai4hpc - updated_at: 1702873408.0 + updated_at: 1704002551.0 openhpc/ohpc: data_format: 2 description: OpenHPC Integration, Packaging, and Test Repo @@ -153507,16 +153508,16 @@ phelelani/nf-rnaSeqMetagen: octicon-link">nf-rnaSeqMetagen @@ -156692,7 +156693,7 @@ powerPlant/apsimx-srf: full_name: powerPlant/apsimx-srf latest_release: null readme: ' @@ -167551,6 +167552,19 @@ remiolsen/pin_hic_singularity: subscribers_count: 1 topics: [] updated_at: 1647940031.0 +repeatexplorer/repex_tarean: + data_format: 2 + description: RepeatExplorer2 singularity definition + filenames: + - Singularity.0.3.7.5996768 + - Singularity.0.3.8.dbaa07f + - Singularity + full_name: repeatexplorer/repex_tarean + latest_release: 0.3.8.2 + stargazers_count: 1 + subscribers_count: 2 + topics: [] + updated_at: 1701766150.0 researchapps/blast: data_format: 2 description: singularity image for biocontainers blast (anaconda) @@ -167859,7 +167873,7 @@ researchapps/sherlock: readme: "This is a repository for container build\ @@ -175271,7 +175285,7 @@ scibian/singularity-container: tabindex="-1" href="#singularityce">SingularityCE
@@ -176941,7 +176955,7 @@ sequana/sequana: - singularity/Singularity.0_8_0 full_name: sequana/sequana latest_release: v0.16.4 - stargazers_count: 134 + stargazers_count: 136 subscribers_count: 6 topics: - ngs @@ -176953,7 +176967,7 @@ sequana/sequana: - snakemake - coverage - rna-seq - updated_at: 1703055863.0 + updated_at: 1703912799.0 sequana/variant_calling: data_format: 2 description: null @@ -180860,8 +180874,8 @@ singularityhub/singularity-deploy: description: Build and deploy Singularity containers to GitHub releases, and pull with the singularity-hpc client filenames: - - Singularity - Singularity.salad + - Singularity - Singularity.pokemon full_name: singularityhub/singularity-deploy latest_release: 0.0.12 @@ -180965,7 +180979,7 @@ singularityhub/singularity-deploy: 0.0.1\"\n \"pokemon\": \"0.0.1\"\nmaintainer: \"@vsoch\"\nurl: https://github.com/singularityhub/singularity-deploy\n\ \n(This part is still under development!)
\n" stargazers_count: 14 - subscribers_count: 5 + subscribers_count: 6 topics: [] updated_at: 1675889215.0 singularityhub/singularity-in-docker: @@ -185650,7 +185664,7 @@ sylabs/singularity: tabindex="-1" href="#singularityce">SingularityCE @@ -185878,13 +185892,13 @@ sylabs/singularity: found in the license file. ' - stargazers_count: 590 + stargazers_count: 597 subscribers_count: 13 topics: - containers - hpc - linux - updated_at: 1703303791.0 + updated_at: 1703984217.0 sylvainschmitt/singularity-octopus: data_format: 2 description: 'octopus Singularity container ' @@ -186349,11 +186363,11 @@ tanushreebanerjee/paquette_2019: data_format: 2 description: null filenames: - - diplomacy_research/containers/ubuntu-cuda10/Singularity - - diplomacy_research/containers/redis/Singularity + - diplomacy_research/containers/research/Singularity - diplomacy_research/containers/albert-ai/Singularity + - diplomacy_research/containers/redis/Singularity + - diplomacy_research/containers/ubuntu-cuda10/Singularity - diplomacy_research/containers/tensorflow-serving/Singularity - - diplomacy_research/containers/research/Singularity full_name: tanushreebanerjee/paquette_2019 latest_release: null readme: "High-performance implementation of real-space\ \ Random Phase Approximation for\ncalculation of plasmonic excitations. For more\ @@ -192537,17 +192551,17 @@ uncch-rdmc/singularity-dev-images: data_format: 2 description: null filenames: - - gephi/Singularity.0.9.2 - - gephi/Singularity.0.9.1 - jupyter/Singularity - jupyter/Singularity.4.4.0 - - anaconda2/Singularity - anaconda2/Singularity.5.3.0 - - rstudio/Singularity.3.5.1 - - rstudio/Singularity + - anaconda2/Singularity - rstudio/Singularity.3.4.4 - - anaconda3/Singularity + - rstudio/Singularity + - rstudio/Singularity.3.5.1 - anaconda3/Singularity.5.3.0 + - anaconda3/Singularity + - gephi/Singularity.0.9.2 + - gephi/Singularity.0.9.1 full_name: uncch-rdmc/singularity-dev-images latest_release: null readme: '