Unable to download EMBOSS on Mac OS
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7.3 years ago
Olivier ▴ 440

I want to install  EMBOSS on a mac, but I'm unable to download it from ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.5.7.tar.gz.

I've sent a request for information from the EMBOSS support team, but I keep getting automatically-generated feedback from their "Mail Delivery Subsystem".
Does anybody know why or have another way around? Thanks

intended platform: Mac OS X 10.9

EMBOSS • 8.5k views
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7.3 years ago
Neilfws 49k

I guess their server is just down right now. They'll probably fix it on Monday :)

If you're desperate, version 6.6.0 seems to be available at this mirror. I discovered that using homebrew:

brew search emboss
homebrew/science/emboss
brew install homebrew/science/emboss
Cloning into '/usr/local/Library/Taps/homebrew/homebrew-science'...
remote: Reusing existing pack: 5491, done.
remote: Total 5491 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (5491/5491), 1.40 MiB | 248.00 KiB/s, done.
Resolving deltas: 100% (2849/2849), done.
Checking connectivity... done.
Tapped 329 formulae
==> Downloading ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz

curl: (28) Connection timed out after 5040 milliseconds
Trying a mirror...
==> Downloading https://science-annex.org/pub/emboss/EMBOSS-6.6.0.tar.gz
######################################################################## 100.0%
==> ./configure --prefix=/usr/local/Cellar/emboss/6.6.0 --enable-64 --with-thread
==> make install
EMBOSS release 6.6.0.0: update information not available
make[3]: *** [install-exec-hook] Error 1
make[2]: *** [install-exec-am] Error 2
make[1]: *** [install-am] Error 2
make: *** [install-recursive] Error 1

READ THIS: https://github.com/Homebrew/homebrew/wiki/troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
  https://github.com/homebrew/homebrew-science/issues

 

The make error at the end is because the install runs embossupdate, which cannot currently connect to the server. You can also download and try the regular ./configure, make, make install.

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The emboss formula has been updated to avoid running embossupdate from make install, so it should be installable while http://emboss.open-bio.org/updates is down.

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7.3 years ago
hpmcwill ★ 1.2k

The current EMBOSS release distribution can be downloaded from the mirror on the EMBL-EBI FTP site.

Automatically generated documentation for the EMBOSS release can be found on the EMBOSS SourceForge site. While this is not a comprehensive as the manuals available on the EMBOSS Open-Bio site, it is much better than nothing :-).

As I understand it from the EMBOSS folks, they are aware of the issues with the Open-Bio site are are working with the Open-Bio admins (see http://www.open-bio.org/ ) to get the issues addressed. At the moment, while the EMBOSS FTP and web sites are unavailable, the EMBOSS mailing lists appear to be back up (see http://mailman.open-bio.org/mailman/listinfo/emboss ). See the EMBOSS mailing list archives for updates on the status of the web and FTP sites, as well as other discussion relating to the programs in EMBOSS and their use.

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3.0 years ago
AK ★ 2.0k

homebrew-science is deprecated.
Switching to Brewsci/bio via brew install brewsci/bio/emboss works.

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