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@bwalsh
bwalsh / dockerized-tools-checklist.md
Created May 27, 2015 16:53
Cookbook for Galaxy Tool integration with local docker registry

Dockerized Tool Installation Checklist

Note: the following instructions have been validated with a CentOS 6.6 virtual machine

Overview

This document outlines the installation of Docker clients (v1.6), a Docker registry (v2.0), approaches on updating Nginx configurations, and testing methodologies for verifying Dockerized tools work in Galaxy.

Installing Docker on compute and gateway nodes

@bwalsh
bwalsh / g2p_issue_discussion.rst
Last active March 10, 2016 20:32 — forked from malisas/g2p_issue_discussion.rst
Comparing implementation choices between Ensembl and OHSU servers, and discussing how schema needs to be better defined.

Roadmap

Guidance

1) Feature's featureType field does not require term

Ensembl's server: All fields in featureType (which is of type OntologyTerm) are present, e.g.:

@bwalsh
bwalsh / gist:71d80d0d4ee97ac176cc
Last active March 14, 2016 22:20 
"featureType": {
   "id": "http://purl.obolibrary.org/obo/SO_0001059"
}
@bwalsh
bwalsh / biodata-elastic-setup.diff
Created April 15, 2016 15:59
Initial setup of new biodata backend for elasticsearch
# git diff
diff --git a/ga4gh/datamodel/datasets.py b/ga4gh/datamodel/datasets.py
index 25f3f7f..c07537e 100644
--- a/ga4gh/datamodel/datasets.py
+++ b/ga4gh/datamodel/datasets.py
@@ -358,3 +358,66 @@ class FileSystemDataset(AbstractDataset):
except KeyError as err:
raise exceptions.MissingDatasetMetadataException(
metadataFileName, str(err))
+
@bwalsh
bwalsh / sparql-query.py
Created June 7, 2016 20:37
python snippet to test sparql queries (use in REPL)
# python snippet to test sparql queries
# set up the graph
import rdflib
_rdfGraph = rdflib.ConjunctiveGraph()
_rdfGraph.parse('tests/data/datasets/dataset1/phenotypes/cgd/cgd-test.ttl', format='n3')
# substitute your query here
@bwalsh
bwalsh / swagger.yml
Last active November 21, 2016 18:21
ya-dms swagger
info:
title: YA-DMS API description
description: |-
### "Yet Another Data Management Service"
##### Key endpoints
![image](https://cloud.githubusercontent.com/assets/47808/20463919/517044ca-aef2-11e6-8d8a-3b1a1f24a1f4.png)
@bwalsh
bwalsh / dcc-portal-changes-12-18
Last active January 9, 2017 18:55
diff --git a/dcc-portal-ui/app/scripts/auth/js/auth.js b/dcc-portal-ui/app/scripts/auth/js/auth.js
index d5f6d81..5663a8e 100644
--- a/dcc-portal-ui/app/scripts/auth/js/auth.js
+++ b/dcc-portal-ui/app/scripts/auth/js/auth.js
@@ -47,7 +47,6 @@
user.verifying = false;
console.log('ohsutoken present');
user.token = ohsutoken;
@bwalsh
bwalsh / dcc-testing-config.patch
Created January 9, 2017 20:57
ui changes not committed to git
diff --git a/dcc-portal-ui/app/develop/scripts/config.js b/dcc-portal-ui/app/develop/scripts/config.js
index 5fb070c..5923632 100644
--- a/dcc-portal-ui/app/develop/scripts/config.js
+++ b/dcc-portal-ui/app/develop/scripts/config.js
@@ -1,9 +1,9 @@
// Global $ICGC_DEV_CONFIG used for dev environment
// profile
global.$ICGC_DEV_CONFIG = {
- // Set DEVELOPER_LOCAL_MODE to true to turn on local developer profile
- // for the 'grunt server' task
@bwalsh
bwalsh / webpack production build...
Created January 9, 2017 23:20
git diff tasks/start.js
diff --git a/dcc-portal-ui/tasks/start.js b/dcc-portal-ui/tasks/start.js
index b508b1d..f41a190 100644
--- a/dcc-portal-ui/tasks/start.js
+++ b/dcc-portal-ui/tasks/start.js
@@ -10,7 +10,7 @@ var execSync = require('child_process').execSync;
var opn = require('opn');
var detect = require('./utils/detectPort');
var prompt = require('./utils/prompt');
-var config = require('../config/webpack.config.dev');
@bwalsh
bwalsh / gist:1afea0a2499b5e81c507dbc24521038e
Created October 30, 2018 21:41
minio s3 config
# cat ~/.aws/credentials
[default]
aws_access_key_id = XXXXXXXXX
aws_secret_access_key = XXXXXX
# cat ~/.aws/config
[default]
region = us-east-1
s3 =
signature_version = s3v4