https://github.com/Sage-Bionetworks-Workflows/nf-tool-synapseclient
synapseclient cli wrapped in nextflow
https://github.com/Sage-Bionetworks-Workflows/nf-tool-synapseclient
Last synced: 20 days ago
JSON representation
synapseclient cli wrapped in nextflow
- Host: GitHub
- URL: https://github.com/Sage-Bionetworks-Workflows/nf-tool-synapseclient
- Owner: Sage-Bionetworks-Workflows
- Created: 2020-05-12T20:05:40.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2021-07-21T09:17:05.000Z (almost 4 years ago)
- Last Synced: 2024-11-16T22:32:50.696Z (6 months ago)
- Language: Nextflow
- Homepage:
- Size: 9.77 KB
- Stars: 0
- Watchers: 9
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Codeowners: .github/CODEOWNERS
Awesome Lists containing this project
- awesome-synapse - nextflow Synapse Client - Nextflow interface to Synapse command line. (Workflow / Shiny)
README
# synapse-nextflow
This is the nextflow tool that wraps `synaspeclient` cli.
```
nextflow pull Sage-Bionetworks/synapse-nextflow
nextflow run Sage-Bionetworks/synapse-nextflow --help
```
If you have conda installed locally, but don't have a conda synapse env, you can leverage the `conda` profile. This creates a local conda environment wherever you are running this `nextflow` command.
```
nextflow run Sage-Bionetworks/synapse-nextflow --command get --synapseconfig ~/.synapseConfig --synid syn18081597 -profile condals
```
If you want to run commands via docker
```
nextflow run Sage-Bionetworks/synapse-nextflow --command get --synapseconfig ~/.synapseConfig --synid syn18081597 -profile docker
```
## AWS
Using aws:
```
aws-saml --profile sandbox-admin
aws --profile sandbox-admin s3 ls s3://tyu-nextflow-test
aws --profile sandbox-admin s3 cp .synapseConfig s3://tyu-nextflow-test
```