1. Ted Liefeld
  2. Combined

Source

Combined /

Filename Size Date modified Message
DevOps
IdentityManager
IdentityManager-Migration/src/main/resources/identityServer
atm
atm-messages
atm-properties
bulkmailer
bulkmailer-properties
caching-support
cdk
cdk-custom-dependencies
cdk-osgi-test
client-config
config
converter-adj2xgmml
converter-api
converter-attr2gmattr
converter-cdt2gct
converter-cdt2tab
converter-example
converter-externalprogramwrapper
converter-externalprogramwrapper-example
converter-galaxyregulators2genesettab
converter-gct2cytoscapeattr
converter-gct2exp
converter-gct2gctx
converter-gct2gctx-custom-dependencies
converter-gct2gmt
converter-gmt2genomicatab
converter-lst2genesettab
converter-odf2cytoscapeattr
converter-res2genesettab
converter-services-api
converter-services-domain
converter-services-with-service-loader
converter-transform
dataformat-repos
dm-converters
dm-converters-examples
dm-core
dm-jobs
dm-jobs-properties
dm-messages
dm-security
dm-webservice
dm-webservice-properties
dropbox-java-sdk
googledrive-test
identityServer
identityServer-common
identityServer-messages
identityServer-properties
ipython_prototype
javascriptCDK/prototypes
jersey-apache-client-osgi
jersey-json-configuration
jsui
jsui-custom-dependencies
jsui-properties
jupyter-notebook
mongo-support
openIdClient
osgi-test-framework
root-webapp
servers-common
servers-common-custom-dependencies
servers-common-logging
test-framework
test-support
typica
usageLogger
util-CommandEngine
virgo-bundle-parent
1.1 KB
Tweak .hgignore to account for the needs of jupyter-notebook project. Allow Typescript ambient files, don't allow generated Javascript files and working files created by Jupyter when running notebooks
1.2 KB
Updating CDK version number
3.9 KB
README.md edited online with Bitbucket
12.7 KB
Added bulkmailer-properties as module to main Maven project.

Build environment

Operating System

We develop, build and test on a regular basis on MacOS and variants of RedHat/CentOS/Amazon Linux.

Java 1.8

We recommend setting the JAVA_HOME environment variable

Maven 3.x

Mercurial (any somewhat recent version)

Runtime Environment

Tomcat 7.x

You will need to configure to utilize SSL. Please consult Tomcat SSL documentation for more info on this.

Also, make the following modification to your catalina.properties under $TOMCAT_HOME/conf to extend the classpath for each server component WAR file

catalina.properties:shared.loader=${catalina.base}/gs-config,${catalina.base}/gs-config/dm-converters/*.jar

Set TOMCAT_HOME in your environment if you would like to use Maven to deploy locally.

Mongo 2.6.x

We expect that more recent versions of Mongo will work, but have not tested them.

Amazon AWS S3

The default main file object repository is S3. You need to create or reuse a an S3 bucket and configure for CORS support as described at the end of this document

Google Drive (optional)

More later

Dropbox (optional)

More later

GenomeSpace client applications

These are not part of GenomeSpace per se, but GenomeSpace is meant to enable applications to interact in the cloud. You will need to install and configure each application that you want to have communicate with your GenomeSpace setup. A list of the applications currently Gs-Enabled can be found here: GenomeSpace Tools and Data Sources

To build all GenomeSpace components:

Create a master properties file. If not specified in the build command line, our Maven build will look for it under:

$HOME/genomespace/env-dev.properties

You will also need in the same directory. It will contain your AWS credentials: genomespace-aws.properties

And to configure the Java GS client while executing the tests: gs-server-url.properties

You will find an annotated templates for this file in this repository under the config directory.

Configuring caching

The checked in code base for GenomeSpace is currently hard-coded to do cache replication via JMS in a clustered environment.

This might not be what you want to do. If this is the case you will need to edit the following files: atm/src/main/resources/ehcache.xml dm-jobs/src/main/resources/ehcache.xml dm-webservice/src/main/resources/ehcache.xml

And remove the strings that match the following two regex expressions:

<cacheManagerPeerProviderFactory(?:.|\r?\n)*?/>

<cacheEventListenerFactory(?:.|\r?\n)*?/>

Maven command to build mvn clean install -Denv-properties-file=MASTERPROPERTIESFILE -Dorg.genomespace.env=URLPROPERTIESFILE

Optional/useful command line options:

-PdeployToLocalTomcat Will copy the GenomeSpace server components, the configuration files, and converters to $TOMCAT_HOME. Note that some tests, such as those that include the Client Development Kit depend on GS being initially deployed.

-DskipTests Standard Maven flag to skip tests

-fae Will run all tests/continue build even if some tests fail. It is likely you will need this flag if you run tests as we still have in our code base tests that are hardcoded with our testing infrastructure setup.

-DskipDropboxTests=false Will skip tests related to Dropbox

-DskipGoogleDriveTests=false Will skip tests related to Google Drive

Support

If you have problems or questions you can reach us at:

gs-help@broadinstitute.org

or post a message to the Genomespace User Forum