# 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 application.properties file located in $PORTAL_HOME--see the deployment manual. If your cBioPortal instance does not yet contain a application.properties file, you can copy src/main/resources/application.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.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 (https://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.	user-guide/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.left_logo	sets the left 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.left_logo value has to contain the folder, e.g. skin.right_logo = myFolder/myImage.jpg	cBioPortal Logo	text
skin.right_logo	sets the right institute 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	no 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.right_nav.show_web_tours	set the "Interactive Tours" section in the right navigation bar	true	true / false
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.show_gsva	enables gsva to query	false	true / false
skin.geneset_hierarchy.default_p_value	modifies default value for p_value threshold	0.05	0.05
skin.geneset_hierarchy.default_gsva_score	modifies default value for gsva_score threshold	0.5	0.5
skin.geneset_hierarchy.collapse_by_default	collapses the tree widget of the gsva hierarchy dialog on init	false	true / false
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
skin.patientview.filter_genes_profiled_all_samples	sets default setting for the genes filter in patient view to only show mutations for genes that were profiled for mutations or CNA's in all samples of that patient. If unset, patient view will show mutations/CNA's for genes that were profiled in any sample.	false	true / false
skin.hide_download_controls	controls download options in UI. true: hides all download options. false: shows all download options. data: disable data download but not figure download	false	true / false / data
download_group	controls download options in UI for each user. If present and user is authenticated, this value is checked against user roles. If the download_group is present in user groups then download options are shown in UI, else it fallback to skin.hide_download_controls		text
skin.show_settings_menu	controls the appearance of the settings menu in study view and group comparison that controls annotation-based filtering.	false	true / false
skin.hide_logout_button	controls the appearance the logout button on a portal with user authentication.	false	true / false
google_analytics_profile_id	enables google analaytics tracking on your site	disabled	string

# Customization when using Docker

To add images or other files to the Docker image one can mount them inside the cbioportal-webapp folder. For example to use a custom logo for skin.right_logo. Mount the image inside thecbioportal-webapp folder with -v /path/to/custom_logo.png:/cbioportal-webapp/images/custom_logo.png and set skin.right_logo=custom_logo.png in your properties file.

# 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:

Copy <cbioportal_source_folder>/portal/src/main/webapp/content/news.html to news_XXXX.html
Modify news_XXXX.html as needed.
Edit the application.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