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brewsci / homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
http://brewsci.github.io/homebrew-bio
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Aragorn server is down, also prevents installation of prokka #1655

Open robmcooper opened 7 months ago

robmcooper commented 7 months ago

I am trying to install prokka, but the first dependency, Aragorn cannot be loaded because its server is down: ==> Fetching brewsci/bio/aragorn ==> Downloading http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.38.tgz curl: (7) Failed to connect to mbio-serv2.mbioekol.lu.se port 80 after 6187 ms: Couldn't connect to server

This is a site-specific problem; my internet works for other sites.

I found an alternative source of Aragorn at http://www.ansikte.se/ARAGORN/Downloads/, compiled it, and placed the binary in my /usr/local/bin folder, which is on my PATH. However, Homebrew does not recognize this non-brew version of Aragorn, and still tries to download from the dead server.

Is there a way to do any of the following?

  1. Fix the Aragorn formula to pull from the working server, which also includes a more updated version (1.2.41 vs 1.2.38 in the Homebrew formula)?
  2. Remove the Aragorn dependency from Prokka, since the Prokka man page actually lists Aragorn as recommended but not required?
  3. Or get Homebrew to recognize Aragorn installed on my PATH, but outside of Homebrew?