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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Prokka install fails because Aragorn website is down. #679

Open ranitori opened 10 months ago

ranitori commented 10 months ago

Hi,

I'm currently trying to install Prokka, but as the website for Aragorn is down, this fails. Below is the readout.

Is there an alternative way for me to install Prokka?

I'm using a MacBook Air with M1 chip. Thanks

% brew install brewsci/bio/prokka ==> Fetching dependencies for brewsci/bio/prokka: brewsci/bio/aragorn, xz, bedtools, hmmer, brewsci/bio/barrnap, ca-certificates, openssl@3, berkeley-db, gdbm, perl, bioperl, lmdb, libomp, blast, brewsci/bio/infernal, giflib, libpng, freetype, fontconfig, pcre2, gettext, glib, xorgproto, libxau, libxdmcp, libxcb, libx11, libxext, libxrender, lzo, pixman, cairo, graphite2, icu4c, harfbuzz, jpeg-turbo, lz4, zstd, libtiff, little-cms2, openjdk, brewsci/bio/minced, parallel, prodigal and brewsci/bio/tbl2asn

==> Fetching brewsci/bio/aragorn

==> Downloading http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.38

curl: (7) Failed to connect to mbio-serv2.mbioekol.lu.se port 80 after 6205 ms: Couldn't connect to server

Error: prokka: Failed to download resource "aragorn"

Download failed: http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.38.tgz

mohmmmdnoman commented 10 months ago

Getting same problem here.

robmcooper commented 9 months ago

Same problem, Aragorn server is down.

I found an alternate way to install Aragorn here http://www.ansikte.se/ARAGORN/Downloads/. After compiling (with warnings) and verifying the binary is callable, I tried brew installing prokka again, but it still wants to pull aragorn from the failed server. Is there any way to tell the prokka installer that aragorn is already installed? Or since the prokka readme says Aragorn is only recommended but not required, is there a way to skip it in the "formula"?

AlbertoLupatin commented 6 months ago

I've found a way to solve this problem common to newer Macs running on arm chips.

I've created a new environment that emulates x64 packages on arm through this code CONDA_SUBDIR=osx-64 conda create -n my_env_name. If you want all future environments to emulate x64, simply omit conda create... from the above code. In this way we could install and run packages available for non-arm computers, such as Prokka.

After creating and activating the new environment, execute this code: conda config --env --set subdir osx-64 and then proceed to install Prokka by typing conda install prokka.

Hope this helps!

mariacadavid commented 3 months ago

@AlbertoLupatin the solution you propose is perfect! Thank you

dopig commented 2 months ago

I am very grateful for prokka's existence over the years! Still getting the same errors as @ranitori who started this thread (today as well as another attempt a few months ago). If the home-brew install isn't going to be maintained, as it depends on an external module that's been offline for >7 months, can/should prokka be taken off homebrew altogether?