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
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
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