Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Unexpected error when running 'bionode' #9

tseemann opened this issue Mar 2, 2015 · 4 comments

Unexpected error when running 'bionode' #9

tseemann opened this issue Mar 2, 2015 · 4 comments


Copy link

@tseemann tseemann commented Mar 2, 2015

I did a global install of bionode, which installed /usr/bin/bionode in my $PATH.

When I run "bionode" I get this error:

Please check the documentation at
        throw er; // Unhandled 'error' event
Error: spawn ENOENT
    at errnoException (child_process.js:1001:11)
    at Process.ChildProcess._handle.onexit (child_process.js:792:34)

Is this expected behaviour?

I notice it downloaded and installed a bunch of tools, and I can see them in /usr/lib/node_modules/bionode/node_modules/ including a subfolder bionode-ncbi but I don't have any tool called bionode-ncbi I can run?

I've never really used npm/Node software before, so any help appreciated.

Copy link

@c089 c089 commented Apr 3, 2015

Hi Torsten, first of all, sorry for the slow response!

Is this expected behaviour?

Well... In a way ;) After reproducing and looking at the code I found that it's expected behavior, but a very unhelpful error message, which we should improve: bionode-ncbi expects you to pass some arguments, e.g. bionode ncbi search taxonomy solenopsis. See the for more usage examples.

I hope this fixes your problem!

Copy link

@tseemann tseemann commented Apr 3, 2015

Do you want me to submit a new issue to improve the error message?

Here's some suggestions on improving the interface:

Copy link

@c089 c089 commented Apr 4, 2015

Thanks for the link. I talked to @bmpvieira last night about replacing the library that is currently used for argument parsing so that we can easily have things like usage info, argument validation, etc. I'll create a new issue later, probably against bionode/bionode as this affects all sub-projects.

Copy link

@bmpvieira bmpvieira commented Apr 4, 2015

Thanks @tseemann. This is one of those obvious issues that should have been fixed by now but hasn't due to lack of time and also because of the minimal library used for parsing arguments (minimist). As @c089 said, we'll switch to a more full-blown parser (yargs) and add this.

Since it's not limited to bionode-ncbi, I'm closing this and you can follow the new issue at bionode/bionode#25.

In the meantime, you can check each module's which links to the documentation (e.g., bionode-ncbi docs) and the global docs at, resulting from the concatenation of all individual html docs (WIP: bionode/bionode#27).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Linked pull requests

Successfully merging a pull request may close this issue.

None yet
3 participants