Unable to Install bactabolize==1.0.2 Due to Missing blast 2.12.0 Dependency

[YahyaFarooqi]

While trying to create a new environment and install bactabolize==1.0.2 using Mamba, I encountered an issue stating that the package could not be installed due to a missing blast 2.12.0 dependency.

I'm running:

mamba create -n bactabolize -y -c scwatts -c bioconda -c conda-forge 'bactabolize==1.0.2'

And I get:

Looking for: ['bactabolize==1.0.2']

conda-forge/osx-arm64 Using cache
conda-forge/noarch Using cache
pkgs/main/osx-arm64 No change
bioconda/noarch No change
bioconda/osx-arm64 No change
pkgs/r/noarch No change
pkgs/main/noarch No change
pkgs/r/osx-arm64 No change
scwatts/osx-arm64 No change
scwatts/noarch No change
Could not solve for environment specs
The following package could not be installed
└─ bactabolize 1.0.2 is not installable because it requires
└─ blast 2.12.0 , which does not exist (perhaps a missing channel).
(base) user@M4819 Bactabolize %

Any help would be appreciated. I'm running on mac M1.

[bananabenana]

Hi @YahyaFarooqi

That is strange as Blast 2.12.0 is part of the conda recipe.
I am not able to replicate this issue on two independent Linux systems. When running the following command I get a clean install:

# Create and activate environment via mamba
mamba create -n bactabolize -y -c scwatts -c bioconda -c conda-forge 'bactabolize==1.0.2'
conda activate bactabolize

# Test installation
bactabolize -h

If this isn't working for you, maybe try to conda install blast prior.

mamba create -n bactabolize -y
mamba install -n bactabolize -y -c bioconda blast=2.12.0
mamba install -n bactabolize -y -c scwatts -c bioconda -c conda-forge 'bactabolize==1.0.2'

Let us know if this fixes the issue.
Thanks

[jotech]

i think the issue is related to the missing arm64 support of bioconda!
but there seems to be some progress in recent weeks: bioconda/bioconda-recipes#23454

[YahyaFarooqi]

@jotech that's probably it i suppose?

@bananabenana here is the output I get when I try your suggestion:

(base) nfarooqi@M4819 ~ % mamba create -n bactabolize -y


Looking for: []

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

To activate this environment, use

     $ mamba activate bactabolize

To deactivate an active environment, use

     $ mamba deactivate

(base) nfarooqi@M4819 ~ % mamba install -n bactabolize -y -c bioconda blast=2.12.0


Looking for: ['blast=2.12.0']

pkgs/r/osx-arm64                                              No change
bioconda/osx-arm64                                            No change
pkgs/main/osx-arm64                                           No change
pkgs/main/noarch                                              No change
pkgs/r/noarch                                                 No change
conda-forge/noarch                                  12.4MB @  13.4MB/s  0.8s
conda-forge/osx-arm64                                7.2MB @   7.6MB/s  0.8s
bioconda/noarch                                      4.7MB @   3.8MB/s  1.3s
Could not solve for environment specs
The following package could not be installed
└─ blast 2.12.0**  does not exist (perhaps a typo or a missing channel).
(base) nfarooqi@M4819 ~ % 

Any chance for a workaround? Maybe through a local install of blast?

[bananabenana]

You can just clone the repo as per our wiki, then install dependancies without conda: https://github.com/kelwyres/Bactabolize/wiki/2.-Installation#direct-install

So local versions of required dependancies, making sure they're available on your path.

Alternatively, other versions of blast will probably be okay too. I can try to nail down some compatible blast versions next week. If you don't want to wait that long, try conda installing alternative blast versions (newer).

[YahyaFarooqi]

Thanks for the suggestion, cloning worked!