More portal.properties Settings
This page describes the main properties within portal.properties.
​Database Settings​
​cBioPortal Customization​
​Segment File URL​
​Google Analytics​
​Password Authentication​
​OncoKB integration​
​CIViC integration​
​OncoPrint​
​Ehcache Settings​
db.user=db.password=db.host=[e.g. localhost to connect via socket, or e.g. 127.0.0.1:3307 to connect to a different port like 3307. Used by Java data import layer]db.portal_db_name=[the database name in mysql, e.g. cbiodb]db.driver=[this is the name of your JDBC driver, e.g., com.mysql.jdbc.Driver]
Include db_connection_string with the format specified below, and replace localhost by the value of db.host:
db.connection_string=jdbc:mysql://localhost/
db.tomcat_resource_name is required in order to work with the tomcat database connection pool and should have the default value jdbc/cbioportal in order to work correctly with the your WAR file.
db.tomcat_resource_name=jdbc/cbioportal
Settings controlling which tabs (pages) to hide. Set them to false if you want to hide those tabs, otherwise set the properties to true.
skin.show_data_tab=skin.show_web_api_tab=skin.show_r_matlab_tab=skin.show_tutorials_tab=skin.show_faqs_tab=skin.show_news_tab=skin.show_tools_tab=skin.show_about_tab=
Note: skin.show_tools_tab refers to the Visualize Your Data tab, while skin.show_data_tab refers to the Data Sets tab.
The cross cancer study query default is a list of studies used when querying one or more genes and not specifying a specific study or list of studies. There are two ways in which the default cross cancer study list is used:
When using the linkout links without a study e.g.
/ln?q=TP53:MUT. Thoselinks are used mostly used to allow for easy linking to particular queries.
One can't get those links using the cBioPortal user interface itself, they
are only mentioned in the documentation of the Web API
In the quick search when querying for a gene. Quick search is
disabled by default. It is a beta feature. See the
The configuration is set with the following if you have session service enabled:
default_cross_cancer_study_session_id=
The title will be pulled from the virtual study. Make sure to create a virtual_study with studies that everybody has access to and don't use a main_session id.
If session service is disabled one can use the following instead:
# query this comma separated list of studiesdefault_cross_cancer_study_list=default_cross_cancer_study_list_name=
Enable or disable the quick search with the following:
# Enable/Disable quick search (default is false)quick_search.enabled=true
The default studies queried when searching for a single gene is defined with the default_cross_cancer_study_session_id or default_cross_cancer_study_list properties as described in the cross cancer study query default section.
Settings controlling what to show in the right navigation bar. Set them to false if you want to hide those sections, otherwise set the properties to true.
#Cancer Studies section:skin.right_nav.show_data_sets=​#Example Queries section:skin.right_nav.show_examples=​#Testimonials section:skin.right_nav.show_testimonials=​#What's New sectionskin.right_nav.show_whats_new=
Setting controlling the blurb: you can add any HTML code here that you want to visualize. This will be shown between the cBioPortal menu and the Query selector in the main page.
skin.blurb=
Setting controlling the citation below the blurb: you can add any HTML code here that you want to visualize. If the field is left empty, this HTML code will be shown: Please cite: <a href="http://cancerdiscovery.aacrjournals.org/content/2/5/401.abstract" target="_blank">Cerami et al., 2012</a> & <a href="http://www.ncbi.nlm.nih.gov/pubmed/23550210" target="_blank">Gao et al., 2013</a>).
skin.citation_rule_text=
Setting controlling the footer: you can add any HTML code here that you want to visualize. If the field is left empty, the default footer (from www.cbioportal.org) will be shown.
skin.footer=
Settings controlling the "What's New" blurb in the right navigation bar: you can add any HTML code here that you want to visualize. If the field is left empty, the Twitter timeline will be shown (as long as skin.right_nav.show_whats_new is true, otherwise this section will not be displayed).
skin.right_nav.whats_new_blurb=
Add a custom logo in the right side of the menu. Place here the full name of the logo file (e.g. logo.png). This file should be saved in $PORTAL_HOME/portal/images/.
skin.right_logo=
Different samples of a patient may have been analyzed with different gene panels. In patient view mutations and discrete CNA's can be filtered based on whether the gene of respective mutations/CNA's was profiled in all samples of the patient (mutations profiled in all samples), or not (mutations profiled in any sample). Setting this field to true will make patient view select the all samples filter at startup. When set to false or left blank the patient view will default to the any samples filter setting.
skin.patientview.filter_genes_profiled_all_samples=
The Mutations tab contains various links, redirecting the user to external information resources regarding the displayed transcript. The Ensembl template URL can be customized by modifying the property:
ensembl.transcript_url=
The default setting is http://ensembl.org/homo_sapiens/Transcript/Summary?t=<%= transcriptId %>. The <%= transcriptId %> is substituted by the frontend code into respective transcript ID.
This is a root URL to where segment files can be found. This is used when you want to provide segment file viewing via external tools such as IGV.
segfile.url=
The following properties are used to provide shortened bookmarks to the cBioPortal:
bitly.user=bitly.api_key=
To obtain a bitly username and key, first register at: https://bitly.com/​
Then, go to: https://bitly.com/a/your_api_key​
Note: If you are developing on a local machine, and using localhost, the bitly URL shortening service will not work. This is because bitly will not shorten URLs for localhost. Once you deploy to your final server, the issue should go away.
If you so desire, the following property is used to track your site's usage via google analytics.
google_analytics_profile_id
The portal supports password authentication via Google+. Before you start you need to setup a google account that will own the authentication API. Follow https://developers.google.com/identity/sign-in/web/devconsole-project to get clientID and secret. Fill it in portal.properties:
googleplus.consumer.key=195047654890-499gl89hj65j8d2eorqe0jvjnfaxcln0.apps.googleusercontent.comgoogleplus.consumer.secret=2jCfg4SPWdGfXF44WC588dK
(note: these are just examples, you need to get your own) You will also need to go to "Google+ API" and click Enable button. In case of problems make sure to enable DEBUG logging for org.springframework.social and org.springframework.security.web.authentication.
To activate password authentication follow the Deployment with authentication steps and set authenticate=googleplus.
In addition, set this property in portal.properties:
app.name=cbioportal
app.name should be set to the name of the portal instance referenced in the "AUTHORITY" column of the "AUTHORITIES" table. See the User Authorization for more information.
OncoKB integration can be turned on or off with the following property (default: true):
show.oncokb=true|false
A private token is required to access the OncoKB Data (for details see the section OncoKB Data Access):
oncokb.token=
CIViC integration can be turned on or off with the following property (default: true):
show.civic=true|false
The CIViC API url is set to https://civic.genome.wustl.edu/api/ by default. It can be overridden using the following property:
civic.url=
Genome Nexus provides annotations of mutations in cBioPortal. The mutations tab relies heavily on the Genome Nexus API, therefore that tab won't work well without it. By default cBioPortal will use the public Genome Nexus API, such that no extra configuration is necessary.
Genome Nexus supports both GRCh37 and GRCh38, but support for the latter is limited. Several annotation sources served by Genome Nexus might not have official GRCh38 support yet i.e. OncoKB, CIViC, Cancer Hotspots, My Cancer Genome and 3D structures. Although most of the time the canonical transcript for a gene will be the same between GRCh37 and GRCh38 there might be some that cause issues. In addition the complete integration of cBioPortal with Genome Nexus' GRCh38 is not complete yet. That is cBioPortal currently only connects to one Genome Nexus API by default (the GRCh37 one), so it's not possible to have multiple genome builds in one instance of cBioPortal and get the correct annotations from Genome Nexus for both. Currently only the mutation mapper tool page is able to handle both.
By default the Genome Nexus API url is set to https://v1.genomenexus.org/, which uses GRCh37. It can be overridden using the following property:
genomenexus.url=
The mutation mapper tool page can annotate GRCh38 coordinates. By default it uses https://grch38.genomenexus.org. It can be overridden by setting:
genomenexus.url.grch38=
The GRCh38 annotation in mutation mapper can be hidden by setting show.mutation_mappert_tool.grch38=false, by default it's set to true;
MDACC Heatmap integration (button in OncoPrint heatmap dropdown and tab on Study page can be turned on or off by setting the following property:
show.mdacc.heatmap=true
The default view in OncoPrint ("patient" or "sample") can be set with the following option. The default is "patient".
oncoprint.defaultview=sample
cBioPortal supports 2 formats to add custom annotations for driver and passenger mutations. 1. cbp_driver: This will define whether a mutation is a driver or not. 2. cbp_driver_tiers: This can be used to define multiple classes of driver mutations.
These data formats are described in the cBioPortal MAF specifications.
To enable functionality for one or both types of custom annotations, enter values for the following properties. These labels will appear in the OncoPrint's "Mutation color" menu.
oncoprint.custom_driver_annotation.binary.menu_label=Custom driver annotationoncoprint.custom_driver_annotation.tiers.menu_label=Custom driver tiers
OncoKB and Hotspots are by default automatically selected as annotation source, if show.oncokb and show.hotspots are set to true. To add automatic selection of custom driver or custom driver tiers annotations, set the respective property to true. Default is false.
oncoprint.custom_driver_annotation.binary.default=true|falseoncoprint.custom_driver_annotation.tiers.default=true|false
If you want to disable the automatic selection of OncoKB and hotspots as annotation source, set these properties to false:
oncoprint.oncokb.default=true|falseoncoprint.hotspots.default=true|false
By default, the selection box to hide VUS mutations is unchecked. If you want to automatically hide VUS, set this property to true. Default is false.
oncoprint.hide_vus.default=true|false
To change the gene sets used for gene querying, create a JSON file and add gene sets, following the format specified in the examples below. Set the path to this file (e.g. file:/cbioportal/custom_gene_sets.json) in the following property and restart Tomcat to apply the update. The default gene sets will be replaced by the ones in custom_gene_sets.json.
querypage.setsofgenes.location=file:/<path>
In this example, two gene sets will appear in the query page, under the names "Prostate Cancer: AR Signaling" and "Prostate Cancer: AR and steroid synthesis enzymes".
[{"id": "Prostate Cancer: AR Signaling","genes": ["SOX9", "RAN", "TNK2", "EP300", "PXN", "NCOA2", "AR", "NRIP1", "NCOR1", "NCOR2"]}, {"id": "Prostate Cancer: AR and steroid synthesis enzymes","genes": ["AKR1C3", "AR", "CYB5A", "CYP11A1", "CYP11B1", "CYP11B2", "CYP17A1", "CYP19A1", "CYP21A2", "HSD17B1", "HSD17B10", "HSD17B11", "HSD17B12", "HSD17B13", "HSD17B14", "HSD17B2", "HSD17B3", "HSD17B4", "HSD17B6", "HSD17B7", "HSD17B8", "HSD3B1", "HSD3B2", "HSD3B7", "RDH5", "SHBG", "SRD5A1", "SRD5A2", "SRD5A3", "STAR"]}]
In this example, only one gene set will appear in the query page, under the name "Genes with alterations", which will add the different genetic alterations stated below in the query box.
[{"id": "Genes with alterations","genes": ["TP53: MUT=R273C;", "KRAS: HOMDEL MUT=NONSENSE MUT=NONSTART MUT=NONSTOP MUT=FRAMESHIFT MUT=SPLICE MUT=TRUNC;"]}]
In this example, only one gene set will appear in the query page, under the name "BRCA genes test", containing the merged gene track called "BRCA genes".
[{"id": "BRCA genes test","genes": ["[\\\"BRCA genes\\\" BRCA1: MUT=E1258D;", "BRCA2: HOMDEL MUT=NONSENSE MUT=NONSTART MUT=NONSTOP MUT=FRAMESHIFT MUT=SPLICE MUT=TRUNC;]"]}]
This gene set will add the following in the query box:
"BRCA genes" BRCA1: MUT=E1258D; BRCA2: HOMDEL MUT=NONSENSE MUT=NONSTART MUT=NONSTOP MUT=FRAMESHIFT MUT=SPLICE MUT=TRUNC;
cBioPortal is supported on the backend with Ehcache. The configuration, size, and location of these caches are configurable from within portal.properties through the following properties.
The cache type is set using ehcache.cache_type. Valid values are none, heap (heap-only), disk (disk-only), and hybrid (disk + heap). By default, ehcache.cache_type is set to none which disables the cache. When the cache is disabled, no responses will be stored in the cache.
ehcache.cache_type=[none or heap or disk or hybrid]
Ehcache initializes caches using a template found in an Ehcache xml configuration file. When caching is enabled, set ehcache.xml_configuration to the name of the Ehcache xml configuration file. The default provided is ehcache.xml; to change the cache template, directly edit this file. Alternatively, you can create your own Ehcache xml configuration file, place it under /persistence/persistence-api/src/main/resources/ and set ehcache.xml_configuration to /[Ehcache xml configuration filename].
ehcache.xml_configuration=
If the cache is configured to use disk resources, users must make a directory available and set it with the ehcache.persistence_path property. Ehcache will create separate directories under the provided path for each cache defined in the ehcache.xml_configuration file.
ehcache.persistence_path=[location on the disk filesystem where Ehcache can write the cache to /tmp/]
Cache size must be set for heap and/or disk depending on which are in use; Ehcache requires disk size to be greater than heap size in a hybrid configuration. Zero is not a supported size and will cause an exception. Units are in megabytes. Default values are provided. The general repository cache is specified to use 1024MB of heap and 4096MB of disk. The static repository cache is specified to use 30MB of heap and 32MB of disk. For installations with increased traffic or data, cache sizes can be increased to further improve performance.
ehcache.general_repository_cache.max_mega_bytes_heap=ehcache.general_repository_cache.max_mega_bytes_local_disk=​ehcache.static_repository_cache_one.max_mega_bytes_heap=ehcache.static_repository_cache_one.max_mega_bytes_local_disk=
Logged metrics and additional information such as cache size and cached keys are available through an optional endpoint. The optional endpoint is turned off by default but can be turned on by setting cache.statistics_endpoint_enabled to true.
cache.statistics_endpoint_enabled=false[true or false]
The cache statistics endpoint is hidden on the api page; users must directly access the URL to view the response. The cache statistics endpoint can be accessed in the following ways.
For general statistics about the cache such as memory usage:
/api/cacheStatistics
For a list of all keys in the cache:
/api/[name of cache]/keysInCache
For a list of counts of keys in cache per repository class:
/api/[name of cache]/keyCountsPerClass
WARNING: It must be noted that since cache statistics endpoint returns data on cache keys, the endpoint may expose otherwise hidden database query parameters such as sample identifiers, study names, etc. Generally, it is recommended that the endpoint only be turned on during cache-related development for testing. Deployers of a protected portal where users only have authorities to a subset of studies should carefully consider whether or not to turn on the cache statistics endpoint, as it does not filter the results.
For more information on Ehcache, refer to the official documentation here​
For more information on how Ehcache is implemented in cBioPortal refer to the Caching documentation.
​GSVA functionality can be enabled by uncommenting this line (and making sure it is set to true):
skin.show_gsva=true
