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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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Difficulty installing anvio v5 #895

Closed mkhall closed 6 years ago

mkhall commented 6 years ago

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 Upgrading 1 outdated package, with result: merenlab/anvio/anvio 2.3.2 -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?

Sofie8 commented 6 years ago

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?

meren commented 6 years ago

Can you please try this:

conda install -n anvio5 -c bioconda -c conda-forge anvio=5.1.0 diamond bwa
meren commented 6 years ago

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

Sofie8 commented 6 years ago

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:

Close matches found; did you mean one of these?

libgcc-ng: libgcc
meren commented 6 years ago

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

Sofie8 commented 6 years ago

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!

meren commented 6 years ago

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

aschuerch commented 6 years ago

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 https://github.com/bioconda/bioconda-recipes/pull/11005

meren commented 6 years ago

Thank you very much for checking, @aschuerch!

charlie-durant commented 5 years ago

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? :)

Luyang-1987 commented 4 years ago

When installing anvio with conda followed the http://merenlab.org/2016/06/26/installation-v2/ and when came to the step: conda install -y -c conda-forge -c bioconda anvio==6.2

it always gave the errors:

Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.

meren commented 4 years ago

hi @Luyang-1987, I haven't heard of this error before, but recently @AstrobioMike shared with me his solution here:

https://hackmd.io/@astrobiomike/anvio-v6-2-conda

Perhaps you should consider trying it. Please let us know re: how it goes.

Best wishes,

AstrobioMike commented 4 years ago

hiya, @Luyang-1987, I'll also note it's not unusual for conda to show those messages as it's checking different ways it might be able to do what it needs to do. Depending on what i'm installing and my current system, i often see those first two pop up and "fail" before moving onto the next way it tries (which usually finishes fine).

It was only after still trying to solve the environment for a long time (with no program-stopping error), that I came up with that other workaround on that linked page