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Difficulty installing anvio v5 #895

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mkhall opened this Issue Jun 28, 2018 · 10 comments

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mkhall commented Jun 28, 2018

I have anvio v4 installed on my computer, and I tried to install v5 with homebrew, and this is what happened:
michellehallenbeck$ brew upgrade anvio
==> Upgrading 1 outdated package, with result:
merenlab/anvio/anvio 2.3.2 -> 5
Warning: Use prodigal instead of deprecated homebrew/science/prodigal
Warning: Use hmmer instead of deprecated homebrew/science/hmmer
Warning: Use hdf5 instead of deprecated homebrew/science/hdf5
Warning: Use diamond instead of deprecated homebrew/science/diamond
Error: No available formula with the name "homebrew/science/mcl" (dependency of merenlab/anvio/anvio)

I checked to make sure I actually have v4 installed:
anvi-profile --version
Anvi'o version ...............................: 4
Profile DB version ...........................: 23
Contigs DB version ...........................: 10
Pan DB version ...............................: 8
Genome data storage version ..................: 6
Auxiliary data storage version ...............: 2

And I also checked to make sure I had MCL installed:
michellehallenbeck$ mcl --version
mcl 14-137
Copyright (c) 1999-2014, Stijn van Dongen. mcl comes with NO WARRANTY
to the extent permitted by law. You may redistribute copies of mcl under
the terms of the GNU General Public License.

I'm not really sure what's going on. Can someone help me fix this?

@mkhall mkhall closed this Jun 28, 2018

@Sofie8

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Sofie8 commented Jul 9, 2018

Hi Meren,

I was trying to install anvio5 via conda: "conda install -c bioconda -c conda-forge anvio diamond bwa", but the version it installs is anvio4. Specifying anvio=5 also didn't do it. And when I do conda update anvio, also anvio4 it shows as most recent. If I download the source file, and run pip install -r requirements.txt and then python setup.py install, it exits with many errors. Can you help me with this issue?

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meren commented Jul 9, 2018

Can you please try this:

conda install -n anvio5 -c bioconda -c conda-forge anvio=5.1.0 diamond bwa
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meren commented Jul 9, 2018

(it would be great if you can report back whether it worked or not)

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Sofie8 commented Jul 9, 2018

Yes, I tried, and I get this:

vsc31426@hpc-p-login-2 /vsc-hard-mounts/leuven-data/314/vsc31426/miniconda3/bin 16:55 $ conda install -n anvio5 -c bioconda -c conda-forge anvio=5.1.0 diamond bwa
Fetching package metadata .............
Solving package specifications:

PackageNotFoundError: Dependency missing in current linux-64 channels:

  • anvio 5.1.0* -> h5py >=2.8.0rc1 -> libgcc-ng >=4.9

Close matches found; did you mean one of these?

libgcc-ng: libgcc
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meren commented Jul 9, 2018

This is unfortunately beyond me, and I will have to summon our conda guru/angel @jmeppley :(

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Sofie8 commented Jul 10, 2018

Hi,
I also searched further and found some suggestions here: #780

I now specified explicitly django=2.0.2, which made it work in my case, for an hpc system.
Hope it is useful for others as well!

./conda create -y --name anvio5 python=3.6
./conda install -y --name anvio5 django=2.0.2
./conda install -y --name anvio5 -c bioconda -c conda-forge anvio=5 diamond bwa

source activate anvio5
anvi-self-test --suite mini

Thanks!

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meren commented Jul 10, 2018

Thank you very much, @Sofie8! You're the best. I updated the installation manual with a note.

@aschuerch

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aschuerch commented Sep 18, 2018

When installing anvio with conda with

conda install -c bioconda -c conda-forge anvio diamond bwa

it also installed the latest hmmer version which gave the error

Config Error: The last call did not work quite well. Most probably the version of HMMER you have installed is not up-to-date enough. Just to make sure what went wrong please take a look at the log file ('/tmp/7982501.1.default/tmpv182ma72/00_log.txt'). Please visit http://hmmer.janelia.org/download.html to see what is the latest version availalbe. You can learn which version of HMMER you have on your system by typing 'hmmpress -h'

when running the self-test.

Downgrading to version 3.1b2 with

conda install hmmer=3.1b2

solved the problem
I put in a pull request to fix this in the recipe bioconda/bioconda-recipes#11005

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meren commented Sep 18, 2018

Thank you very much for checking, @aschuerch!

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charlie-durant commented Dec 19, 2018

Thank you very much, @Sofie8! You're the best. I updated the installation manual with a note.

Yes, thank you! This ended up working for me (on a Linux VM) too, but I spent a while trying to figure out why anvi'o commands couldn't be found before I saw the 'source activate anvio5' line here. Could this also be included in the installation instructions? :)

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