Customizing your cBioPortal Instance via portal.properties

Customizing your instance of cBioPortal

cBioPortal contains a number of properties that allow you to customize your cBioPortal instance.

This page focuses on the skin properties, which allow you to customize the web page cosmetics, such as custom images, texts, which tabs are visible, etc. Nearly all the skins properties have defaults, which can be overwritten by changing the portal.properties file located in $PORTAL_HOME--see the deployment manual. If your cBioPortal instance does not yet contain a portal.properties file, you can copy src/main/resources/portal.properties.EXAMPLE and edit it.

Below you can find the complete list of all the available skin properties.

cBioSkins Properties

Please note! If you are reading this on the GitHub web site, you may need to scroll right to see all the columns in the table below.

Name

Description

Default

Type Allowed

skin.authorization_message

sets the authorization message that appears after an unsuccessful login

Access to this portal is only available to authorized users at Memorial Sloan Kettering Cancer Center...

Any HTML text

skin.blurb

sets the main text on the index page

Text for public cBioPortal.org.

Any HTML text

skin.custom_header_tabs

defines custom tabs to be added to the header. For each page to be added, two values have to be provided. The first is the page, the second the tab-title. e.g. skin.custom_header_tabs=networks.jsp, Networks, oncoprinter.jsp, Oncoprinter

comma separated text

skin.example_study_queries

\n-separated list of study query suggestions displayed when clicking the ‘select a cancer study' search box

tcga\ntcga -provisional\ntcga -moratorium\ntcga OR icgc\n-"cell line"\nprostate mskcc\nesophageal OR stomach\nserous\nbreast

text separated by the escape sequence \n

skin.data_sets_footer

sets the text that is shown below the number of samples, after clicking on the "DATA SETS" tab in the header.

The portal currently contains data from the following cancer genomics studies. The table below lists the number of available samples per data type and tumor.

Any HTML text

skin.data_sets_header

sets the text that is shown below the Data Sets title, after clicking on the "DATA SETS" tab in the header. By adding <NUM_CANCER_STUDIES> to the text, the number of cancer studies is inserted

Data sets of TCGA studies were downloaded from Broad Firehose (http://gdac.broadinstitute.org) and updated monthly. In some studies, data sets were from the TCGA working groups directly.

Any HTML text

skin.documentation.about

set the about page which can be accessed via ABOUT in the header. Please see the cBioportal Documentation section for details on how to properly configure the documentation pages.

About-Us.md

text

skin.documentation.baseurl

set the base url for the documentation. Please see the cBioPortal Documentation section for details on how to properly configure the documentation pages.

https://github.com/cBioPortal/cbioportal/wiki/

text

skin.documentation.faq

set the faq page which can be accessed via FAQ in the header. Please see the cBioPortal Documentation section for details on how to properly configure the documentation pages.

FAQ.md

text

skin.documentation.markdown

set whether the documentation files are in markdown. Please see the cBioPortal Documentation section for details on how to properly configure the documentation pages.

true

text

skin.documentation.news

set the news page which can be accessed via NEWS in the header. Please see the cBioPortal Documentation section for details on how to properly configure the documentation pages.

News.md

text

skin.email_contact

sets the contact email address for Questions and feedback, located in the footer.

cbioportal at googlegroups dot com

Specify as name at somewhere dot extension or as name@somewhere.extension

skin.examples_right_column_html

set the Examples Queries section in the right navigation bar

<ul><li><a href="patient?studyId=ucec_tcga_pub&caseId=TCGA-BK-A0CC">Patient view of an endometrial cancer case</a></li></ul>

Any HTML text

skin.footer

sets the footer text. The text will be appended to the already existing cBioPortal link

cBioPortal public instance footer.

Any HTML text

skin.login.contact_html

sets the feedback message which appears after a failed login attempt

If you think you have received this message in error, please contact us at...

Any HTML text

skin.login.saml.registration_html

sets the button text for saml login

Sign in with MSK

Any HTML text

skin.right_logo

sets the right logo in the header. Logo should be placed in the images directory or in a subdirectory of the images directory. If placed in a subfolder, the skin.right_logo value has to contain the folder, e.g. skin.right_logo = myFolder/myImage.jpg

MSKCC Logo

text

skin.right_nav.show_data_sets

show the "Data Sets" section in the right navigation bar

true

true / false

skin.right_nav.show_examples

show the "Example Queries" section in the right navigation bar

true

true / false

skin.right_nav.show_testimonials

show the "What People are Saying" section in the right navigation bar

true

true / false

skin.right_nav.whats_new_blurb

set the content of the "What’s New" section in the right navigation bar

Text for public cBioPortal.org.

Any HTML text

skin.show_about_tab

show the "ABOUT" tab in the header

true

true / false

skin.show_data_tab

show the "DATA SETS" tab in the header

true

true / false

skin.show_faqs_tab

show the "FAQ" tab in the header

true

true / false

skin.show_news_tab

show the "NEWS" tab in the header

true

true / false

skin.show_r_matlab_tab

show the "R/MATLAB" tab in the header

true

true / false

skin.show_tools_tab

show the "TOOLS" tab in the header

true

true / false

skin.show_tutorials_tab

show the "TUTORIALS" tab in the header

true

true / false

skin.show_web_api_tab

show the "WEB API" tab in the header

true

true / false

skin.tag_line_image

sets the tag line image in the header. The image should be placed in the images directory or in a subdirectory of the images directory. If placed in a subdirectory, the skin.tag_line_image value has to contain the folder, e.g. skin.tag_line_image = myFolder/myImage.jpg

tag_line.png

text

skin.title

sets the title of the site / name of the browser tab. E.g. when navigating to About Us with the default setting, the title becomes "cBioPortal for Cancer Genomics::About Us"

cBioPortal for Cancer Genomics

text

skin.query.max_tree_depth

sets the maximum number of subcategories shown in the query component hierarchy before each study. E.g. when set to 0, the hierarchy is flat, meaning only the study elements show in the component, without any tissue or cancer type sorting.

3

integer

Creating your own local news/about or FAQ page

Creating you own local news/about or FAQ page involves three steps. For example, to create your own news page:

  1. Copy <cbioportal_source_folder>/portal/src/main/webapp/content/news.html to news_XXXX.html

  2. Modify news_XXXX.html as needed.

  3. Edit the portal.properties file and change the skin.documentation.news property, giving it the name of your news HTML component.

You may need to modify additional settings depending on whether you're e.g. using markdown pages. Please refer to the cBioPortal Documentation for more information.

cBioPortal Documentation Settings

cBioPortal supports internal as well as external pages and supports html and markdown pages.

Using External Pages

cBioPortal can retrieve external pages and use them as news/faq/about page. For example, if your news page is stored on github wiki and reachable via https://github.com/cBioPortal/cbioportal/wiki/News.md use

skin.documentation.baseurl=https://github.com/cBioPortal/cbioportal/wiki/
skin.documentation.news=News.md

Using Internal Pages

cBioPortal can use pages stored in (a subdirectory of) your content directory as news/faq/about page. For example, if your news page is called myNews.md and stored in content/myFolder, use

skin.documentation.baseurl=/
skin.documentation.news=myFolder/myNews.md

Markdown

By default, cBioPortal assumes all documentation is in markdown. If your documentation is not in markdown, please use

skin.documentation.markdown=false

If your documentation contains a relative link, cBioPortal will assume it uses the same format and, when clicked, will try to interpret the page as such. If your documentation contains an absolute link, cBioPortal will open it in a new window when clicked. Please be aware that the links may be case-sensitive! E.g. https://github.com/cBioPortal/cbioportal/wiki/News.md is not the same as https://github.com/cBioPortal/cbioportal/wiki/news.md

Custom styling of the patient view's clinical data

The Patient View shows several clinical attributes at the top of the page, e.g. AGE, SEX: test The order, styling and visibility of those attributes at the top can be changed by editing the patient view's clinical attributes CSS file.