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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.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.
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 [email protected]
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.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.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.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:
    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
1
skin.documentation.baseurl=https://github.com/cBioPortal/cbioportal/wiki/
2
skin.documentation.news=News.md
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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
1
skin.documentation.baseurl=/
2
skin.documentation.news=myFolder/myNews.md
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Markdown

By default, cBioPortal assumes all documentation is in markdown. If your documentation is not in markdown, please use
1
skin.documentation.markdown=false
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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:
The order, styling and visibility of those attributes at the top can be changed by editing the patient view's clinical attributes CSS file.
Last modified 2mo ago