Error in rule generate_consensus_sequences V1.2.1, V1.2.5

[jeroencremer]

Dear Developers,

Installation command: mamba create -n piranha -c bioconda piranha-polio=1.2.1 -y
Installation command: mamba create -n piranha-V2.5 -c bioconda piranha-polio=1.2.5 -y
The installs of both versions seem to be going well.

It look like the same problem as "issue #236 " but now with the command line versions of Piranha.
We seem to have the same problem with both versions V1.2.1 and 1.2.5
This sample works with the piranhaGUI version 1.2.1

errorV1.2.1.txt
errorV1.2.5.txt

Thanks in advance for the help.

Jeroen Cremer

[rmcolq]

I've just merged in the PR which had fixes to the environment file and docker image. Hopefully that will soon solve your problem - not released yet as there are a few more unrelated changes in progress at the moment which will very shortly be done.

[jeroencremer]

Dear Developers,

Installation command: mamba create -n piranha -c bioconda piranha-polio=1.3 -y

It look like the same problem as "issue #236 " but now with the command line versions of Piranha.
The problem still seems to be present in version 1.3

Thanks in advance for the help.

error.txt

[rmcolq]

To be clear - are you installing the environment file first? Or just installing piranha from bioconda?

[jeroencremer]

Installing piranha from bioconda.

With the environment file we have a problem with "Failed to build medaka pyspoa"
Failed to build medaka pyspoa.txt

[rmcolq]

What operating system are you using? Are you able to run in a Docker container instead of on the command line?

I'm not sure what the process is for generating the bioconda recipe, but I know that there is a problem with a version of medaka which pip installs several packages in such a way that is incompatible with some computer architectures (including mac M1 and some linux).

Could you resend that error, it's not loading

[jeroencremer]

We have an linux LSF-based computer cluster.
It's not possible to use the docker container on our netwerk.
On my private laptop, it runs fine

Failed to build medaka pyspoa.txt

[rmcolq]

You could try mirroring the additional steps I took in the Dockerfile in your conda environment and see if they fix it for you too:

pip uninstall -y tensorflow keras pyabpoa
conda install -y -c conda-forge tensorflow~=2.11 keras~=2.11

Note that the issue is that pip installing these packages results in incompatibility with the AVX chipset, whereas they can be installed nicely with conda (except pyabpoa which isn't actually necessary, just results in a warning). I had further unsolvable (within a week) problems with medaka version > 1.12.0, and medaka forces these packages to be installed with pip instead of conda

[rmcolq]

That error also states that medaka failed to be installed because of RuntimeError: Unsupported compiler -- at least C++11 support is needed!

[jeroencremer]

-->(mamba create -n piranha -c bioconda piranha-polio=1.3 -y)
Will it be possible to get the Mamba Pipline working?
to fix the issue with "Error in rule generate_consensus_sequences"
Or will it not be possible to make this work in the short term?

-->(git clone https://github.com/polio-nanopore/piranha.git)
I will try to solve the C++11 problem
to be able to install the pipeline in this way.