Documentation
¶
Overview ¶
Package sources is the single source of truth for all external data URLs that atb downloads. Every URL the tool fetches from the internet is defined here, grouped by feature.
OSF project: https://osf.io/h7wzy/files/osfstorage AllTheBacteria: https://allthebacteria.org
To update a URL: change it here and it propagates everywhere. To audit what atb downloads: read this file.
Index ¶
Constants ¶
const ( SketchSkmFilename = "atb_sketchlib.skm" SketchSkdFilename = "atb_sketchlib.skd" SketchSubdir = "sketch" )
SketchSkmFilename and SketchSkdFilename are local filenames for the sketch database files, stored in <data-dir>/sketch/.
const AssemblyBaseURL = "https://allthebacteria-assemblies.s3.eu-west-2.amazonaws.com/"
AssemblyBaseURL is the S3 bucket hosting individual genome FASTA files. File pattern: {sample_accession}.fa.gz Used by: atb download, atb sketch query --download
const IndexFilename = "all_atb_files.tsv"
IndexFilename is the local cache filename for the OSF file index.
const IndexURL = "https://osf.io/download/r6gcp/"
IndexURL is the master TSV index listing ~3,000 files across the entire AllTheBacteria project on OSF, with download URLs and MD5 checksums. Used by: atb osf ls, atb osf download Source: https://osf.io/r6gcp (all_atb_files.tsv)
const SketchSkdURL = "https://osf.io/download/92qmr/"
SketchSkdURL is the sketch data file (.skd) for the aggregated ATB sketch database (~4.1 GB). Used by: atb sketch fetch
const SketchSkmURL = "https://osf.io/download/nwfkc/"
SketchSkmURL is the sketch metadata file (.skm) for the aggregated ATB sketch database covering all genomes up to Aug 2024 (~122 MB). Used by: atb sketch fetch
const SketchlibRepo = "bacpop/sketchlib.rust"
SketchlibRepo is the GitHub repository for sketchlib releases.
const SketchlibVersion = "v0.2.4"
SketchlibVersion is the pinned version of the sketchlib binary.
Variables ¶
var CoreTables = []string{
"assembly.parquet",
"assembly_stats.parquet",
"checkm2.parquet",
"sylph.parquet",
"run.parquet",
"mlst.parquet",
"amrfinderplus.parquet",
}
CoreTables lists the tables downloaded by default with `atb fetch`.
var TableURLs = map[string]string{
"assembly.parquet": "https://osf.io/download/4ku2n/",
"assembly_stats.parquet": "https://osf.io/download/69c51e86801fecc5d6146396/",
"checkm2.parquet": "https://osf.io/download/69c51e93cba7111bb21d27f2/",
"sylph.parquet": "https://osf.io/download/69c51f90cba7111bb21d2905/",
"run.parquet": "https://osf.io/download/69c51f68376eb79a651d2d85/",
"mlst.parquet": "https://osf.io/download/69c66d33fa3d973d94254f46/",
"amrfinderplus.parquet": "https://osf.io/download/69c69298f4dc657ae4253e8b/",
"ena_20250506.parquet": "https://osf.io/download/69c51f3ab4f99c692d54cf73/",
"ena_20240801.parquet": "https://osf.io/download/69c51f002e72f67915145d0e/",
"ena_20240625.parquet": "https://osf.io/download/69c51ec99ce80b96ac54cd08/",
"ena_202505_used.parquet": "https://osf.io/download/69c51f475eedad376954ce7b/",
"ena_661k.parquet": "https://osf.io/download/69c51f57376eb79a651d2d83/",
}
TableURLs maps parquet table filenames to their OSF download URLs.
Functions ¶
This section is empty.
Types ¶
This section is empty.
Source Files