Sean Davis seandavi

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

Install ingress-nginx on aws

Will use ELB
Will use wildcard cert provided by AWS (https://console.aws.amazon.com/acm/)

Install nginx ingress on AWS

This installs a set of resources.

Using helm:

Assumes kubernetes cluster created and kubectl configured correctly.

kubectl create serviceaccount --namespace kube-system tiller
kubectl create clusterrolebinding tiller-cluster-rule --clusterrole=cluster-admin --serviceaccount=kube-system:tiller
helm init --service-account tiller

Install postgresql (available charts at https://github.com/helm/charts/tree/master/stable)

	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);
	}

	# To accompany: https://seandavi.github.io/2019/05/single-cell-packages-and-dependencies-in-bioconductor-using-biocpkgtools/
	library(BiocPkgTools)
	library(igraph)
	library(visNetwork)
	bpl = biocPkgList()
	bpl_sc = bpl[grepl('SingleCell', bpl$biocViews),]
	dep_df = buildPkgDependencyDataFrame()
	dep_graph = buildPkgDependencyIgraph(dep_df)
	dep_graph_sc = inducedSubgraphByPkgs(dep_graph, bpl_sc$Package )
	ledges <- data.frame(color = c("green", "lightblue", "red"),

	digraph Workflow {

	node [shape="box"];

	subgraph cluster_0 {
	SRA_XML [shape=record label="SRA XML\|{Study\|Sample\|Experiment\|Run}"]
	XML_TO_JSON [label="XML to JSON"]
	SRA_JSON [shape=record label="SRA JSON\|{Study\|Sample\|Experiment\|Run}"]
	BIOSAMPLE_XML [label="Biosample XML"]
	BIOSAMPLE_JSON [label="Biosample JSON"]