ncbi-tool-cliclient

• NCBI-replica with version history data storage platform. Phase 1 of creating a service for accessing old versions of NCBI data. For use in the Infectious Disease platform.

Archived

This repository was created for experimental purposes and is no longer maintained or used.

Installation

1. Download the binary for your system:
   • bin/darwin-amd64/ncbitool for Mac
   • bin/linux-amd64/ncbitool for Linux
   • Or build from source: go build -o ncbitool
2. Move to /usr/local if desired. Or run with ./ncbitool command
3. Run chmod u+x ncbitool if any permissions issues.

Usage

• Reference API documentation here.
• Usage:
  • ncbitool command [command options] [arguments...]
  • General file structure on the server is the same as on ftp://ftp.ncbi.nlm.nih.gov/blast/db/
• Commands:
  • file - file actions. Gets file info.
  • directory - directory actions. Gets directory info.
  • help, h - Shows a list of commands or help for one command
• Sub-commands:
  • file at-time - get a file version at or before a point in time
  • file history - get the version history of a file
  • directory at-time - get a directory state at or before a point in time
  • directory compare - compare a directory state across a start and end date
• Flags:
  • Make sure to put flags before the last file path argument.
  • --download - include to download the files to local disk
  • --input-time [value] - input time for 'at time' requests. Ex: 2017-07-07T00:06:12
  • --version-num [value] - version number for file requests
  • --dest [value] - download destination on local disk
  • --help, -h - show help
  • --start-date [value] - start date for directory diff comparisons
  • --end-date [value] - end date for directory diff comparisons
• Example commands:
  • ncbitool file /blast/db/README
  • ncbitool file --download --version-num 3 --dest ~/Desktop /blast/db/README
  • ncbitool file at-time --download --input-time "2017-07-12T08:38:46" /blast/db/nr.00.tar.gz
  • ncbitool file history /blast/db/nr.00.tar.gz
  • ncbitool directory /blast/db/FASTA
  • ncbitool directory --download --dest ~/Desktop /blast/db/FASTA
  • ncbitool directory at-time --download --input-time "2005-07-12T08:38:46" --dest ~/Desktop /blast/db/FASTA
  • ncbitool directory compare --start-date "2015-07-12T08:38:46" --end-date "2017-07-20T08:38:46" /blast/db/FASTA

Development info

1. git clone https://github.com/chanzuckerberg/ncbi-tool-cliclient
2. go get github.com/urfave/cli
3. go build -o ncbitool or env GOOS=linux GOARCH=amd64 go build -o bin/linux-amd64/ncbitool to cross-compile for a specific platform.

Links

• Components:

  • Sync service: https://github.com/chanzuckerberg/ncbi-tool-sync
  • Server service: https://github.com/chanzuckerberg/ncbi-tool-server
  • Command line client: https://github.com/chanzuckerberg/ncbi-tool-cliclient

• Planning docs:

  • Part 1: https://docs.google.com/document/d/1y9Y6Q5HgPHT5CfIPCMtkK2gIINtzcTEhdNzEWwqIIw4/edit
  • Part 2 and API documentation: https://docs.google.com/document/d/1mRzOFqJvhAWb4954o1eV-DVSvm_RFukohnt5bvTch-4/edit