Easier Method to Make a Bioinformatics Pipeline Available on the Web
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3.4 years ago
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I want to make a website that makes a bioinformatics command line application or a pipeline available on the web, but I really do not want to manually make a graphically inconvenient (like quite a lot of servers published) web frontend for each program.
A platform like Mobyle ( http://mobyle.rpbs.univ-paris-diderot.fr ) or Galaxy ( https://usegalaxy.org ) without the provided tools, and providing custom-made tools would be the most plausible, but it should be convenient, and resource-efficient to implement. I want to know if there is a better tool than Galaxy or Mobyle. Also, registration should be optional in order for use.
I have found a tool called WeBIAS ( https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-015-1622-x ), I'm not sure if this fits my use.
Are there any tools that can fulfil this purpose? I have found this link ( https://omictools.com/workflow-management-systems-category ), but I am not sure of which tool to use.
Thank you very much in advance.

bioinformatics web ui pipeline • 1.5k views
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3.4 years ago

The only commonly used tool like this is Galaxy, for which you simply write an XML wrapper for each tool. The pipelines/workflows themselves are also just text files, though honestly I find that easier to create in the UI (or from a history) than manually in a text editor.

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Is it possible to make logins optional and instead incorporate a captcha system like reCAPTCHA or any other methods like this?
Also, how do you consider other programs in this link: https://omictools.com/workflow-management-systems-category (Select "Web user interface" in "Filters"), such as http://www.atgc-montpellier.fr/waves/ https://bioinfo.imdik.pan.pl/webias or Mobyle ?

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You can probably put Galaxy behind a reCATCHA-based filter, but I'm not sure what the point would be. I'd just make it usable without a login.

Regarding the other systems, they're not really used by anyone other than their authors, so I don't see much point in them. There are hundreds of Galaxy servers in the world and a lot of training that goes on in every continent, so it's really the only options if you want to avoid training everyone from scratch and developing integration of a lot of other tools.

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Thanks for your clarification. I was just worried if my server might get spammed or DDOSed.... I think Galaxy is the best option.

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If you need to make this available only for local users then a simple solution is to limit access to your web server using appropriate IP restrictions.

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It'd be tough to spam a Galaxy server, anonymous logins won't see content from each other, so it'd be a pain to use for file transfer. Regarding a DDOS, a reCAPTCHA isn't going to save you from that.

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