orca-5: Remove poretools - brewsci/homebrew-bio#266

[suujia]

remove from orca-5, versions.tsv, and singularity.1

Porecamp: Primary purpose of converting FAST5 to FASTQ files is no longer needed. Albacore does that. NanoPlot can be used for plotting and reporting https://github.com/wdecoster/NanoPlot
It seems to me that we can remove poretools.

-sjackman

https://github.com/brewsci/homebrew-bio/pull/266

[suujia]

Think we can ignore these error messages (but let me know if it should be changed):

 Base images should not use the latest tag.

-- even in docker documentation they use the latest tag when inheriting previous build stage. https://docs.docker.com/develop/develop-images/multistage-build/#before-multi-stage-builds

You should avoid installing or using `sudo` since it has
                                           unpredictable TTY and signal-forwarding behavior that can cause
                                           more problems than it solves.

[sjackman]

Think we can ignore these error messages (but let me know if it should be changed):

Can you please look into configuring dockerfilelint to silence these two types of warnings? I'd like to ignore them so that the TravisCI check would be 🍏

[sjackman]

Can you please link to the original brewsci/bio PR, and include in the commit log the error message and reason that poretools is being removed from ORCA?

[sjackman]

Super confusing, but it looks like there are two similarly named tools: dockerfilelint and dockerfile_lint. We're currently using the former, I believe, though the latter seems more popular. I have no preference. We could switch to the latter if that helps. See https://www.npmjs.com/package/dockerfile_lint and https://www.npmjs.com/package/dockerfilelint and this very helpful blog post: https://jacace.wordpress.com/2016/12/01/tools-to-lint-dockerfiles/

[suujia]

Oh I see. Thanks for the links! I will look into it :P

[sjackman]

I've opened an issue at https://github.com/projectatomic/dockerfile_lint/issues/110 to ask how to override the severity of a default rule.

[sjackman]

Could you please open a new separate PR to change from using dockerfilelint to dockerfile_lint? This PR can then be changed back to its original purpose of removing poretools.

[suujia]

haha sorry for the spam. I will work on that. I have squashed it (and merged) only the poretools. I will make another pull request for dockerfile_lint

[sjackman]

No worries. Thanks for making this fix, Susie.