Introduction | Installation | Supported URL Schemes | Quick Start | Authentication | HTTP/HTTPS | Amazon S3 | S3-compatible services | Google Cloud Storage | Azure Blob Storage | Short-lived tokens: token provider functions | URL-specific credentials | Cache Control | Integration with SeqArray | Session Information
Package: gdscloud 0.99.6
Xiuwen Zheng
gdscloud: Cloud Storage Access for GDS Files
Provides read-only access to GDS (Genomic Data Structure) files stored on cloud storage services including Amazon S3, Google Cloud Storage (GCS), and Azure Blob Storage, as well as any HTTP/HTTPS URL. It extends the 'gdsfmt' package so that cloud URLs (http://, https://, s3://, gs://, az://) can be opened transparently, without downloading the whole file first. Only the blocks that are actually read are fetched, using HTTP Range requests via libcurl together with an in-memory least-recently-used block cache, so that random access to a remote GDS file behaves like access to a local one. Credentials are resolved from the usual environment variables of each service, or set per session and per URL prefix, and they can be exported to the workers of a parallel cluster.
Authors:
gdscloud_0.99.6.tar.gz
gdscloud_0.99.6.zip(r-4.7-x86_64)gdscloud_0.99.6.zip(r-4.7-arm64)gdscloud_0.99.6.zip(r-4.6-x86_64)gdscloud_0.99.6.zip(r-4.6-arm64)gdscloud_0.99.6.zip(r-4.5-x86_64)
gdscloud_0.99.6.tgz(r-4.6-x86_64)gdscloud_0.99.6.tgz(r-4.6-arm64)gdscloud_0.99.6.tgz(r-4.5-x86_64)gdscloud_0.99.6.tgz(r-4.5-arm64)
gdscloud_0.99.6.tar.gz(r-4.7-arm64)gdscloud_0.99.6.tar.gz(r-4.7-x86_64)gdscloud_0.99.6.tar.gz(r-4.6-arm64)gdscloud_0.99.6.tar.gz(r-4.6-x86_64)
gdscloud_0.99.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gdscloud/json (API)
| # Install 'gdscloud' in R: |
| install.packages('gdscloud', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/zhengxwen/gdscloud/issues
Uses libs:
On BioConductor:gdscloud-0.99.5(bioc 3.24)
infrastructuredataimportazurecloudgcsgdss3curlopensslcpp
Last updated from:094075f4ac. Checks:1 WARNING, 15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 131 | ||
| linux-devel-arm64 | OK | 140 | ||
| linux-devel-x86_64 | OK | 211 | ||
| source / vignettes | OK | 250 | ||
| linux-release-arm64 | OK | 152 | ||
| linux-release-x86_64 | OK | 229 | ||
| macos-release-arm64 | OK | 139 | ||
| macos-release-x86_64 | OK | 285 | ||
| macos-oldrel-arm64 | OK | 113 | ||
| macos-oldrel-x86_64 | OK | 198 | ||
| windows-devel-arm64 | OK | 226 | ||
| windows-devel-x86_64 | OK | 259 | ||
| windows-release-arm64 | OK | 247 | ||
| windows-release-x86_64 | OK | 187 | ||
| windows-oldrel-x86_64 | OK | 201 | ||
| wasm-release | OK | 118 |
Exports:gdsCloudCacheCleargdsCloudCacheInfogdsCloudCacheSizegdsCloudConfigAzuregdsCloudConfigGCSgdsCloudConfigHTTPgdsCloudConfigS3gdsCloudExportCredentialsgdsCloudListgdsCloudOpengdsCloudOptionsgdsCloudSchemes
Dependencies:gdsfmt
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Cloud Storage Access for GDS Files | gdscloud-package gdscloud |
| Cache Control for Cloud GDS Access | gdsCloudCacheClear gdsCloudCacheInfo gdsCloudCacheSize |
| Configure HTTP/HTTPS Credentials | gdsCloudConfigHTTP |
| Configure Cloud Storage Credentials | gdsCloudConfigAzure gdsCloudConfigGCS gdsCloudConfigS3 |
| Export Cloud Credentials to Child Processes | gdsCloudExportCredentials |
| List Open Cloud Streams | gdsCloudList |
| Open a GDS File from Cloud Storage | gdsCloudOpen |
| Package Options for Cloud Access | gdsCloudOptions |
| List Supported Cloud URL Schemes | gdsCloudSchemes |