Sean Davis seandavi

Example R API

To use, clone this repository and then run:

Rscript api.R

Test using the following URLs:

Run a Bioconductor Workshop on a Google Cloud Instance

To run one of the workshops for Bioc2020, follow these steps after determining which workshop you'd like to run and finding the docker image name. Substitute the docker image name below for tidytranscriptomics if desired.

Prereqs

A google cloud platform account (which you can create with $300 free credit if you don't have one)
Installed google cloud sdk (the gcloud command)

XML file mirroring

ftp://ftp.ncbi.nlm.nih.gov/sra/reports/Mirroring/

srastatrep (api)

docs

https://www.ncbi.nlm.nih.gov/Traces/sra/status/srastatrep.fcgi

Build an R package

├── DESCRIPTION <<<--- This is the only file needed to have an R package!
├── NAMESPACE
├── R
│   └── hello.R
...
└── man
 └── hello.Rd

	---
	title: "Big Data Approaches"
	subtitle: "Where to go with Bioconductor"
	event: "Bioconductor Technical Advisory Board Meeting"
	#author: Sean Davis
	date: "`r Sys.Date()`"
	output:
	BiocStyle::html_document
	---

	library(tibble)
	library(jsonlite)
	library(curl)
	as_tibble(jsonlite::fromJSON(curl('https://api.omicidx.cancerdatasci.org/sra/studies/ERP009142/runs?size=500'))$hits)

	"""
	Creates, updates, and deletes a job object.
	"""

	from os import path
	import os

	import yaml
	import uuid

	module monitor

	go 1.13

	require (
	github.com/jackc/pgx/v4 v4.1.2
	github.com/jinzhu/gorm v1.9.11
	github.com/joho/godotenv v1.3.0
	go.uber.org/zap v1.13.0
	)

	from elasticsearch import Elasticsearch
	cli = Elasticsearch() # may need to create

	from elasticsearch_dsl import connections
	connections.add_connection('default',cli.client)

	import elasticsearch_dsl as dsl
	class Study(dsl.Document):
	class Index:
	name = 'sra_study-zq'

	class Main {
	public static void main(String[] args) {
	String s1 = "Taylor Swift";
	String s2 = "John Boyega";
	String s3 = "Emma Stone";
	String s4 = s1.substring(2,s1.length()-3).toLowerCase();
	String s5 = s2.substring(2,s2.length()-3).toLowerCase();
	String s6 = s3.substring(2,s3.length()-3).toLowerCase();
	System.out.println(s1 + ">>>" + s4 + "\n" + s2 + ">>>" + s5 + "\n"+ s3 + ">>>" + s6);
	}