Mamba Install Issue

[afvrbanac]

Hello, I'm working on a Mac with an M4 chip and having some trouble installing Bactabolize. Running the command:

mamba create -n bactabolize -y -c kelwyres -c bioconda -c conda-forge 'bactabolize==1.0.4

Gives me the error message:

error libmamba Could not solve for environment specs The following package could not be installed └─ bactabolize ==1.0.4 * does not exist (perhaps a typo or a missing channel). critical libmamba Could not solve for environment specs

Trying the older version with the command:
mamba create -n bactabolize -y -c kelwyres -c bioconda -c conda-forge 'bactabolize==1.0.3'

I get:

error libmamba Could not solve for environment specs The following package could not be installed └─ bactabolize ==1.0.3 * is not installable because it requires └─ blast ==2.12.0 *, which does not exist (perhaps a missing channel). critical libmamba Could not solve for environment specs

[bananabenana]

Hi @afvrbanac ,

Apologies, it appears conda didn't get our 1.0.4 push which fixed these installation issues! I'll fix that and update the readme. In the meantime, please use:

mamba create -n bactabolize -y
mamba install -y -n bactabolize -c bioconda blast==2.12.0
mamba install -y -n bactabolize -c kelwyres -c bioconda -c conda-forge 'bactabolize==1.0.3'

If that doesn't work out of the box, please use:

mamba create -y -n bactabolize
mamba install -y -n bactabolize -c conda-forge python==3.9
mamba install -y -n bactabolize -c conda-forge biopython==1.79
mamba install -y -n bactabolize -c conda-forge glpk==5.0
mamba install -y -n bactabolize -c bioconda blast==2.12.0
mamba install -y -n bactabolize -c conda-forge swiglpk==5.0.10
mamba install -y -n bactabolize -c conda-forge urllib3=2.2.2
mamba install -y -n bactabolize -c conda-forge cchardet==2.1.7
mamba install -y -n bactabolize -c conda-forge tabulator=1.25.1
mamba install -y -n bactabolize -c conda-forge goodtables==2.5.4
mamba install -y -n bactabolize -c conda-forge openpyxl==2.4.11
mamba install -y -n bactabolize -c kelwyres -c bioconda -c conda-forge 'bactabolize==1.0.3'

[bananabenana]

Hi @afvrbanac hopefully this has solved your issue. Please re-open issue if not.

[afvrbanac]

Hi unfortunately I still get the error:

error libmamba Could not solve for environment specs The following package could not be installed └─ bactabolize ==1.0.3 * is not installable because it requires └─ blast ==2.12.0 *, which does not exist (perhaps a missing channel). critical libmamba Could not solve for environment specs

[kelwyres]

Apologies, it seems there is an issue with the automated conda build via GitHub, that I'm unable to fix myself. Please bear with me while I get some advice on this.

Thanks.
Kelly

[bananabenana]

Hi @afvrbanac

We (the talented @scwatts ) has updated Bactabolize to fix this issue

To install, please try running:

mamba create -n bactabolize_1.0.4 -y -c kelwyres -c bioconda -c conda-forge 'bactabolize==1.0.4'

Thanks

[bananabenana]

Closing this. Please reopen if there is any further trouble.

[apreston243]

I also have the same issue:

error libmamba Could not solve for environment specs
The following package could not be installed
└─ bactabolize ==1.0.4 * is not installable because it requires
└─ blast ==2.12.0 *, which does not exist (perhaps a missing channel).
critical libmamba Could not solve for environment specs

Tried the various fixes above, but still gives the same blast 2.12.0 issue.

[bananabenana]

Hi @apreston243 thanks for letting us know. Re-opened.

Are you also on a Mac? This would be the simplest explanation, as the only version of Blast that is compatible with Apple ARM CPUs is 2.16.0. I have confirmed installation works on multiple linux environments.

If you have an Apple ARM CPUs, go to Apple ARM CPU. If not, go to Else.

Apple ARM CPU

I have just updated Bactabolize to 1.0.6, which uses Blast 2.16.0. Please try running:

mamba create -n bactabolize -y -c kelwyres -c bioconda -c conda-forge 'bactabolize==1.0.6'

Else

Could you try the following:

# Identify blast version 2.12.0
conda search -c bioconda blast=2.12.0

If that doesn't come up with something like:

Loading channels: done
# Name                       Version           Build  Channel
blast                         2.12.0      h3289130_1  bioconda
blast                         2.12.0      h3289130_2  bioconda
blast                         2.12.0      h3289130_3  bioconda
blast                         2.12.0      hf3cf87c_4  bioconda
blast                         2.12.0 pl5262h3289130_0  bioconda

Then it may be your conda/mamba cache for channel metadata is outdated. To fix this, you can run:

conda update conda
conda clean --all
conda install mamba -n base -c conda-forge

Now, try reinstalling Bactabolize with the following:

mamba create -n bactabolize -y --override-channels -c kelwyres -c bioconda -c conda-forge -c defaults 'bactabolize==1.0.6'

Let me know how it goes

[apreston243]

Ben Many thanks for the swift and thoughtful response. Yes, I am on a 2022 M2 chip Mac. The search for blast2.12.0 failed, so I tried the clean and reinstall of conda/mamba. On trying to install 1.06, I now get the error that prodigal 2.6.3 does not exist. I appreciate you taking the trouble to try to fix this. Bactabolize is a very valuable tool to create, I remain keen to try it. Regards Andy Professor Andrew Preston Professor of Microbial Pathogenesis The Milner Centre for Evolution and Department of Life Sciences University of Bath Bath BA2 7AY U.K. ***@***.*** +44 1225 386318 http://www.bath.ac.uk/groups/milner-centre-for-evolution/ https://periscope-project.eu On 11 Jun 2025, at 02:43, Ben Vezina ***@***.***> wrote: mamba create -n bactabolize -y --override-channels -c kelwyres -c bioconda -c conda-forge -c defaults 'bactabolize==1.0.6'