Ecosyste.ms: Repos

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Package Usage: pypi: toil

Pipeline management software for clusters.
448 versions
Latest release: 4 months ago
4 dependent packages
6,424 downloads last month

View more package details: https://packages.ecosyste.ms/registries/pypi.org/packages/toil

View more repository details: https://repos.ecosyste.ms/hosts/GitHub/repositories/DataBiosphere%2Ftoil

Dependent Repos 41

SwissDataScienceCenter/renku-python
A Python library for the Renku collaborative data science platform.
  • 5.6.0 poetry.lock
  • ==5.6.0 pyproject.toml

Size: 40.6 MB - Last synced: 10 days ago - Pushed: about 1 month ago

abdo3a/PcG_finder
protein homologous finder
  • ==3.18.0 requirements.txt

Size: 8.07 MB - Last synced: 3 months ago - Pushed: about 1 year ago

EBI-Metagenomics/emg-viral-pipeline
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
  • ==5.4.0 cwl/requirements/pip_requirements.txt

Size: 28.8 MB - Last synced: 3 days ago - Pushed: 4 days ago

Ensembl/python-requirements
Sets of requirements files required to install a tool or setup a virtualenv
  • ==3.16.0 toil/requirements.txt
  • * tony_cwltool/requirements.txt

Size: 37.1 KB - Last synced: 27 days ago - Pushed: about 1 year ago

cloudlinux/libcare
libcare -- Patch Userspace Code in Live Processes
  • ==3.10.1 scripts/toil/requirements.txt

Size: 368 KB - Last synced: 27 days ago - Pushed: over 3 years ago

ComparativeGenomicsToolkit/cactus
Official home of genome aligner based upon notion of Cactus graphs
  • ==5.6.0 toil-requirement.txt

Size: 17.3 MB - Last synced: 3 days ago - Pushed: 3 days ago

ComparativeGenomicsToolkit/hal
Hierarchical Alignment Format
  • ==5.3.0 requirements.txt

Size: 8.43 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

nsoranzo/planemo Fork of galaxyproject/planemo
Command-line utilities to assist in developing tools for the Galaxy project.
  • * dev-requirements.txt

Size: 9.7 MB - Last synced: 29 days ago - Pushed: about 1 month ago

bgruening/planemo Fork of galaxyproject/planemo
Command-line utilities to assist in developing tools for the Galaxy project.
  • * dev-requirements.txt

Size: 9.68 MB - Last synced: 28 days ago - Pushed: about 1 month ago

msk-access/nucleo
Workflow that creates all the BAM files for the cfDNA assay based FASTQ file at MSK
  • * requirements.txt

Size: 915 KB - Last synced: 4 months ago - Pushed: over 1 year ago

frankligy/SNAF
Splicing Neo Antigen Finder (SNAF) is an easy-to-use Python package to identify splicing-derived tumor neoantigens from RNA sequencing data, it further leverages both deep learning and hierarchical Bayesian models to prioritize certain candidates for experimental validation
  • ==3.8.0 AltAnalyze/requirements_all.txt

Size: 86.6 MB - Last synced: 30 days ago - Pushed: about 1 month ago

msk-access/uncollapsed_bam_generation
Workflow for making MSK-ACCESS standard binary alignment mapping file.
  • * requirements.txt

Size: 1.82 MB - Last synced: 10 days ago - Pushed: 11 days ago

bigdatagenomics/workflows
Toil workflows for bigdatagenomics tools. Apache 2 licensed.
  • >=3.8.0 docs/requirements.txt

Size: 155 KB - Last synced: 6 days ago - Pushed: about 3 years ago

sidharth-05/1ACoding
  • ==5.3.0 YoutubeDashboard/requirements.txt

Size: 185 MB - Last synced: 4 months ago - Pushed: over 1 year ago

med-team/virify
CWL-implementation of VIRify pipeline
  • ==5.3.0 cwl/requirements/pip_requirements.txt

Last synced: 27 days ago

msk-access/access_qc_generation
Generation Quality Controls Files for MSK-ACCESS
  • ==5.1.0 requirements.txt

Size: 6.16 MB - Last synced: 4 months ago - Pushed: over 1 year ago

ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit
  • ==5.0 setup.py

Size: 15.3 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

EBI-Metagenomics/CRISPRCasFinder-CWL
Implementation of CRIPSPRCasFinder tool in CWL
  • ==5.5.0 requirements.txt

Size: 236 KB - Last synced: 28 days ago - Pushed: almost 2 years ago

Sage-Bionetworks/amp-workflows
Standardized workflows for AMP-AD data processing and analysis
  • >=3.20.0 amp-rnaseq_reprocessing/amp-rnaseq_reprocess-workflow/Pipfile

Size: 47.9 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago

Kulivox/planemo Fork of galaxyproject/planemo
Command-line utilities to assist in developing Galaxy and Common Workflow Language artifacts - including tools, workflows, and training materials.
  • * dev-requirements.txt

Size: 9.47 MB - Last synced: 8 months ago - Pushed: 8 months ago

Sage-Bionetworks/neurolincsdreamchallenge
  • * workflows/unique-objects-workflow/requirements.txt

Size: 95.7 KB - Last synced: about 1 month ago - Pushed: almost 2 years ago

msk-access/bam_collapsing
Workflow for collapsing of standard binary alignment mapping file generated by MSK-ACCESS
  • ==5.0.0 requirements.txt

Size: 1.62 MB - Last synced: 10 days ago - Pushed: 11 days ago

EMBL-EBI-TSI/cpa-bioexcel-cwl
Cloud Portal Application for bioexcel cwl execution
  • * ostack/ansible/roles/cwl/files/cwl_bioexcel/Pipfile
  • ==5.4.0 ostack/ansible/roles/cwl/files/cwl_bioexcel/Pipfile.lock

Size: 87.9 KB - Last synced: about 1 year ago - Pushed: over 2 years ago

nxwi/illacceptanything Fork of illacceptanything/illacceptanything
The project where literally anything* goes.
  • * data/requirements.txt

Size: 1.33 GB - Last synced: 7 months ago - Pushed: over 1 year ago

genap/chord_wes
  • ==3.20.0 requirements.txt

Size: 988 KB - Last synced: over 1 year ago

GastonLab/ddb-ngsflow
The Dead Drift Bioinformatics NGS Workflow engine. Uses Toil
  • * requirements.txt

Size: 318 KB - Last synced: 21 days ago - Pushed: over 4 years ago

galaxyproject/planemo
Command-line utilities to assist in developing Galaxy and Common Workflow Language artifacts - including tools, workflows, and training materials.
  • * dev-requirements.txt

Size: 10.1 MB - Last synced: 3 days ago - Pushed: 4 days ago

illacceptanything/illacceptanything
The project where literally anything* goes.
  • * data/requirements.txt

Size: 1.47 GB - Last synced: 8 days ago - Pushed: 8 days ago

mskcc/pluto
Utilities for pluto-cwl and helix_filters repos
  • ==5.7.1 environment.yml

Size: 251 KB - Last synced: about 21 hours ago - Pushed: over 1 year ago

mskcc/pluto-cwl
CWL workflows for helix filter scripts
  • ==5.7.1 environment.yml

Size: 1.3 MB - Last synced: about 21 hours ago - Pushed: 10 months ago

msk-access/cwl_subworkflows
A list of subworkflows used for MSK-ACCESS data processing.
  • ==5.7.1 requirements.txt

Size: 907 KB - Last synced: 4 months ago - Pushed: 4 months ago

thiagogenez/cactus Fork of ComparativeGenomicsToolkit/cactus
Official home of genome aligner based upon notion of Cactus graphs
  • ==5.8.0 toil-requirement.txt

Size: 11.3 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

bento-platform/bento_wes
Workflow execution service (based on GA4GH WES schemas) for the Bento platform.
  • 5.8.0 poetry.lock
  • ~5.8 pyproject.toml

Size: 1.36 MB - Last synced: 6 days ago - Pushed: 6 days ago

jvivian/rnaseq-recompute-analysis
Analysis of RNA-seq recompute expression data
  • >=3.6.0 setup.py

Size: 146 MB - Last synced: 22 days ago - Pushed: almost 7 years ago

yifengyou/hotpatch
内核态热补丁、用户态热补丁
  • ==3.10.1 user-hotpatch/libcare/src/scripts/toil/requirements.txt

Size: 1.93 MB - Last synced: 25 days ago - Pushed: almost 2 years ago

ntchambers/illacceptanything
The project where literally anything* goes
  • * requirements.txt

Last synced: over 1 year ago

WEHI-ResearchComputing/wehi-pipeline
Wrapper layer for Toil to create pipelines in the WEHI environment
  • * setup.py

Size: 95.7 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago

007gzs/test
  • * requirements.txt

Size: 1.6 MB - Last synced: 4 months ago - Pushed: 4 months ago

ga4gh/cloud-interop-testing
Interoperable execution of workflows using GA4GH APIs
  • * requirements.txt

Size: 1.29 MB - Last synced: 27 days ago - Pushed: almost 3 years ago

hbeale/ProTECT
  • ==5.4.0 setup.py

Size: 187 KB - Last synced: about 1 year ago - Pushed: about 2 years ago

gijzelaerr/spiel
Astronomical Simulation Pipeline based on CWL
  • * requirements.txt

Size: 283 KB - Last synced: 11 days ago - Pushed: over 4 years ago

gijzelaerr/buis
A Django based web fronted for toil
  • * requirements.txt

Size: 4.35 MB - Last synced: 11 days ago - Pushed: over 4 years ago

GastonLab/ddb-datastore
Variant Storage Service and Database that integrates with the DDBIO workflows tools
  • * requirements.txt

Size: 484 KB - Last synced: 21 days ago - Pushed: over 3 years ago

johnbradley/toil-secondary-bug
Example toil bug
  • ==3.8.0 requirements.txt

Size: 0 Bytes - Last synced: about 1 year ago - Pushed: almost 7 years ago

vidhyaboghara/Semantic-and-Sentiment-Analysis
Sentiment Analysis performed on twitter data and Semantic Analysis performed on News articles extracted from news API
  • * required_files/negative-words.txt

Size: 757 KB - Last synced: about 1 year ago - Pushed: about 4 years ago

jlevy44/ArcticAI
See application demo: https://arcticai.demo.levylab.host.dartmouth.edu/
  • ==5.9.2 arctic_ai.egg-info/requires.txt
  • ==5.9.2 requirements.txt

Size: 76.4 MB - Last synced: 7 days ago - Pushed: about 1 year ago

arunbodd/cactus Fork of ComparativeGenomicsToolkit/cactus
Official home of genome aligner based upon notion of Cactus graphs
  • ==5.9.2 toil-requirement.txt

Size: 15.2 MB - Last synced: 22 days ago - Pushed: about 1 year ago

biozhangzhou/cactus Fork of ComparativeGenomicsToolkit/cactus
Official home of genome aligner based upon notion of Cactus graphs
  • ==4.1.0 toil-requirement.txt

Size: 8.47 MB - Last synced: 10 months ago - Pushed: over 3 years ago

TheBearodactyl/illacceptanything Fork of illacceptanything/illacceptanything
The project where literally anything* goes.
  • * data/requirements.txt

Size: 1.33 GB - Last synced: 10 months ago - Pushed: 10 months ago

BitaoQiu/Comparative-Annotation-Toolkit Fork of ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit
  • >=5.0 setup.py

Size: 15.3 MB - Last synced: 10 months ago - Pushed: over 3 years ago

gijzelaerr/1gc-pipeline
  • * requirements.txt

Size: 23.4 KB - Last synced: 11 days ago - Pushed: over 4 years ago

philge/Comparative-Annotation-Toolkit Fork of ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit
  • ==5.0 setup.py

Size: 15.2 MB - Last synced: 10 months ago - Pushed: almost 3 years ago

hweej/cbx-modules
  • * Pipfile
  • ==4.2.0 requirements.txt

Size: 8.81 MB - Last synced: 27 days ago - Pushed: over 3 years ago

ksuderman/planemo Fork of galaxyproject/planemo
Command-line utilities to assist in developing Galaxy and Common Workflow Language artifacts - including tools, workflows, and training materials.
  • * dev-requirements.txt

Size: 9.79 MB - Last synced: 27 days ago - Pushed: about 1 year ago

justin-ys/CanDIGv2-testing Fork of CanDIG/CanDIGv2
The CanDIG v2 platform
  • ==5.2.0 etc/venv/requirements-dev.txt

Size: 1.28 MB - Last synced: 27 days ago - Pushed: 10 months ago

lynceuslq/emg-viral-pipeline Fork of EBI-Metagenomics/emg-viral-pipeline
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
  • ==5.3.0 cwl/requirements/pip_requirements.txt

Size: 11.6 MB - Last synced: 9 months ago - Pushed: almost 3 years ago

braillescreen/illacceptanything Fork of illacceptanything/illacceptanything
The project where literally anything* goes.
  • * data/requirements.txt

Size: 1.47 GB - Last synced: 9 months ago - Pushed: about 1 year ago

boginw/illacceptanything Fork of illacceptanything/illacceptanything
The project where literally anything* goes.
  • * data/requirements.txt

Size: 1.33 GB - Last synced: 29 days ago - Pushed: 9 months ago

yuanbit/planemo Fork of galaxyproject/planemo
Command-line utilities to assist in developing tools for the Galaxy Project.
  • * dev-requirements.txt

Size: 6.9 MB - Last synced: 27 days ago - Pushed: almost 6 years ago

EveliaCoss/hal Fork of ComparativeGenomicsToolkit/hal
Hierarchical Alignment Format
  • ==4.2.0 requirements.txt

Size: 8.18 MB - Last synced: 9 months ago - Pushed: about 3 years ago

charles-gumbi/cactus Fork of ComparativeGenomicsToolkit/cactus
Official home of genome aligner based upon notion of Cactus graphs
  • ==5.5.0 toil-requirement.txt

Size: 11 MB - Last synced: 9 months ago - Pushed: over 2 years ago

Sisov/Comparative-Annotation-Toolkit Fork of ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit
  • >=3.5 setup.py

Size: 14.2 MB - Last synced: 9 months ago - Pushed: about 6 years ago

AlexFeng123/libcare Fork of cloudlinux/libcare
libcare -- Patch Userspace Code in Live Processes
  • ==3.10.1 scripts/toil/requirements.txt

Size: 368 KB - Last synced: 9 months ago - Pushed: over 3 years ago

mstabrin/planemo Fork of galaxyproject/planemo
Command-line utilities to assist in developing Galaxy and Common Workflow Language artifacts - including tools, workflows, and training materials.
  • * dev-requirements.txt

Size: 9.52 MB - Last synced: 9 months ago - Pushed: 9 months ago

zintown/libcare Fork of cloudlinux/libcare
libcare -- Patch Userspace Code in Live Processes
  • ==3.10.1 scripts/toil/requirements.txt

Size: 370 KB - Last synced: 9 months ago - Pushed: almost 4 years ago

MikeWLloyd/Python_DockerBuild
  • ==4.2.0 requirements.txt

Size: 12.7 KB - Last synced: 19 days ago - Pushed: about 3 years ago

ymxNancy/Comparative-Annotation-Toolkit Fork of ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit
  • ==5.0 setup.py

Size: 15.2 MB - Last synced: 8 months ago - Pushed: almost 3 years ago

darafferty/rapthor
LOFAR DDE pipeline
  • [cwl]>=5.10 pyproject.toml

Size: 3 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

epam/cloud-pipeline
Cloud agnostic genomics analysis, scientific computation and storage platform
  • ==5.3.0 deploy/docker/cp-tools/base/toil/requirements.txt

Size: 165 MB - Last synced: 30 days ago - Pushed: about 1 month ago

datalayer-externals/renku-notebooks Fork of SwissDataScienceCenter/renku-notebooks
An API service to provide jupyter notebooks for the Renku platform.
  • 5.10.0 git_services/poetry.lock

Size: 2.52 MB - Last synced: 6 months ago - Pushed: 6 months ago

RichardJActon/renku-python Fork of SwissDataScienceCenter/renku-python
A Python library for the Renku collaborative data science platform.
  • 5.10.0 poetry.lock
  • ==5.10.0 pyproject.toml

Size: 22.7 MB - Last synced: 5 months ago - Pushed: 5 months ago

btraven00/runner-tinker
work towards benchmark ontology & runner
  • * toil/requirements.txt

Size: 106 KB - Last synced: 5 months ago - Pushed: 5 months ago

jen-dev-basesolve/Toil-Pipeline
Toil Pipeline to align DNA sequences
  • ==5.9.2 requirements.txt

Size: 4.6 MB - Last synced: about 1 year ago - Pushed: about 1 year ago