Tool development tips
Team development and source controlIt's easy for development team members to collaborate on Ghub. All the users listed on the development team of a tool have access to that tool's repo. So,...
Using Python packages from Jupyter Notebooks
The Jupyter tool is a useful place to develop Python, R, or Octave code and analyses in a notebook style. Hub users can easily share their notebooks with other users by publishing notebooks as...
Invoke scripts for Jupyter notebooks
The Ghub tool invoke script is located in the tool's middleware/ subdirectory. When you first create a tool, the basic invoke script provided must be edited to work with Jupyter notebook...
Submit functionality enables qualified users to execute certain codes on the compute cluster. In order to use submit functionality, you must have access to the HUBzero Workspace and be a member of...
A number of environment variables are available in a Ghub tool session. A few are discussed here. A full list can be viewed by running the env command from a terminal in the Workspace tool, the...
Files for tool input and output
While developing tools, we need someplace to store temporary files, calculation results, and data uploaded by users. Here's a brief guide to best practices.Session variableFiles in User...
Jupyter tool deployment styles
How do you want your Jupyter Notebook-based tool to behave when a user runs it? You have several choices, which we describe here:Tool or App Mode style--code cells are hidden, UI widgets are...
Testing Jupyter-based tools
The proxied Jupyter tool is a useful place to develop code and analyses in a notebook style. Ghub users can easily share their notebooks with other users by publishing notebooks as tools. The...
Workflows on Ghub
Documentation and examples of computational pipelines using PegasusExamplesWhat is a scientific workflow?Workflow Examples ShowcaseWorkflow Tools on GhubDocumentationPegasus Workflow...
Publishing Jupyter Notebooks
The Jupyter tool is a useful place to develop code and analyses in a notebook style. Ghub users can easily share their notebooks with other users by publishing notebooks as tools. A published...
Create a Ghub tool with Rappture builder
Note that while this functionality is still available, we recommend using the Jupyter Notebooks (jupyter6deb10) tool to develop user interfaces for your Ghub tools. Refer to the Jupyter Examples...
Tool development workflow
This workflow describes how a Ghub user may develop, test, troubleshoot, and deploy a new tool on the Ghub site. This workflow assumes the user has developed the tool using the C language; the tool...
Hub Tool Directory Structure
When developing tools, use the recommended Ghub tool directory structures and save yourself some grief.Ghub Application Space Directory StructureThis is the actual directory structure of your...
If you are behind a network firewall that requires you to use a web proxy with your browser, your Java environment will also need to use a proxy to connect to tool sessions. The default security...
Earning points in the Questions & Answers forum
Each question in the forum has its own "market" value, which reflects the level of community interest the question has generated. This is calculated by summing up the weighted number of answers,...
Customize your "My HUB" page
To change your "My HUB" page, simply click the Personalize button located in the upper-right corner of that page. The page will enter a customization mode where you may move modules...
Frequently asked questions
What is the difference between public, restricted, and private groups?How do I make a public group private? And vice-versa?How are groups managed?Who can see resources/wiki pages/discussions in a...
Frequently asked questions
What are tags?How do I create a new tag?How can I delete a tag?How can I remove a tag from a resource/group/my profile/etc?Is there a limit on the number of tags I can add to an item?Can I tell...
Group guidelines & tips
Ultimately it is the group Administrators who decide what the rules are for their group, but if you have been made a manager of a group, here are some suggestions for keeping your group...
Help! I'm getting a Java error!
Users may experience a Java error on Mac OS X if they are using Java version 1.3 and below. Please ensure your Java install is up to date.NOTE! For gecko browsers (Mozilla, Firefox, Camino), the...