User_FAQs

bioBakery User FAQs

Thank you for your use of the bioBakery tool suite. This is a collection of FAQs covering general questions about tool use. If you do not see an answer to your question, feel free to reach out to us through our Discourse site.

1. I am new to metagenomic data processing and analysis. Where do I begin?

We suggest checking out the documentation available in the bioBakery wiki. This provides detailed tutorials for all of the tools. More specifically check out the bioBakery workflows which is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. If you have specific questions about a tool feel free to contact us through our Discourse site.

2. I am having issues installing a tool. Where can I go for help?

Sorry to hear you are having issues with installing a tool. Most commonly install issues are related to the install of dependencies of a bioBakery tool which can be difficult based on the environment. The good news is most likely another user has run across this install issue and there is a post and resolution on our Discourse site. Please check it out and if you can't find the solution to your issue please feel free to post and we will be happy to help you with your install issue.

3. I am running into an error running a tool and I don't know how to solve it. Where can I go for help?

Sorry to hear you are seeing an error. Please check out the Discourse site to see if another user has posted the error and it has been resolved. If you don't see any posts that help you resolve your error, please post to the site so we can help you get up and running again.

4. I found an issue with the tool that I need to be resolved. How do I report this?

Sorry for the issue and thank you for reaching out to report the issue. Instead of reporting issues in github we request users report them to our Discourse site. Please first check to see if this issue has already been reported. If it has already been resolved, please update your tool install to the latest release to resolve the error. If the issue has not already been resolved (apologizes if this is the case but this should not likely happen we hope!), please bump the original post on Discourse and we will get it resolved ASAP.

If this is a new issue, please create a new post to Discourse. Please provide the following information to help us recreate and then debug the issue you are seeing: 1) the exact command to create the error 2) information about your install environment (ie conda vs docker and OS) 3) the input files used (reduced in size if possible) 4) the exact error message (eg any tracebacks and logs you can include are helpful). The more information you can provide the faster we can help debug the issue and figure out a solution.

5. I found an issue with the tool and I would like to submit a pull request (PR) to resolve it. How do I do this?

Thank you for finding the issue and also finding the solution. First please check that this issue has not been resolved in the latest version of the tool. If this issue is still open, please check out our forum to confirm that it is not an issue we are currently working on resolving. If this issue is open, it is easily reproducible, you can provide a test case, the amount of code to resolve the issue is less then 10 lines, and does not affect the core computations of the software in anyway, we encourage you to open a pull request. If the issue is open but is difficult to reproduce or the amount of code required to solve the issue is large or the code change will affect the core software computations, we encourage you to post all of the information about the issue to Discourse.

6. I would like to add a new feature to the tool. How do I do this?

We appreciate user feedback and suggestions. Please feel free to post your suggestions to Discourse. We currently can't support user pull requests for new features at this time due to the amount of benchmarking and evaluations required for each feature added to each tool.

If you would like to you can fork our tools and modify them. We just request that you 1) fork the repo instead of copying it into your own repository and 2) make a note in the readme in your forked repository that includes a reference to the original software and states that this is a fork with custom modifications.

7. I would like to help with the development of the tools by submitting PRs. How do I do this?

We are happy to have the help of users to make our tools better through posting issues and feedback and suggestions. We are also happy to review small PRs (10 lines or less with changes not affecting the core computations or functionality) for known issues that are well documented and reproducible. However, we do not encourage new feature PRs from users due to the amount of time spent benchmarking and evaluating each tool for any changes we make before each release.