Customizing your instance of cBioPortal

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}/src/main/resources/portal.properties. If your cBioPortal instance does not yet contain a portal.properties file, you can copy the 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.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	set the Examples Queries section in the right navigation bar. The html page should be placed in the content directory or in a subdirectory of the content directory. If placed in a subdirectory, the skin.examples_right_column value has to contain the folder, e.g. skin.examples_right_column = myFolder/myExamples.html	examples.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.patient_view.show_clinical_trials_tab	show the "Clinical Trials" tab in the patient view	true	true / false
skin.patient_view.show_drugs_tab	show the "Drugs" tab in the patient view	true	true / false
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_visualize_your_data_tab	show the "VISUALIZE YOUR DATA" 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

Creating your own local news/about/FAQ/or Examples page

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

1. Copy {PORTAL_HOME}/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