Problems installing conda package

IFB Core Cluster Demande de logiciel ou de banque de données
1

Bonjour,

I am trying to install the current version of medaka using conda, however, when I do it in the cluster it does not install the current version (1.4.2) but an old obsolete one (1.2.2) that also present some conflicts with some python libraries required. I wonder if this is related to the fact of having an not up to date version of conda

The recipe I am using and that works perfectly in other OS (using conda 4.10.1) is the following one:

conda create -n medaka -c conda-forge -c bioconda medaka

Thanks in advance for the help!, it would be really appreciate it

Jazmin

2

Bonjour Jazmin,

Indeed, I see the same thing on the cluster (but I don't know why):
conda version 4.9.2 installs medaka-1.2.2
conda version 4.10.1 installs medaka-1.4.1

We probably update the module conda on the cluster.
In the meantime, maybe you can install a more recent version of conda: Installing on Linux — conda 4.10.1.post26+e14d58909 documentation

Is it ok for you ?

1 « J'aime »
3

Bonjour,

Thank you so much for the reply I'll try to follow your suggestion and I will keep you informed.

Cheers,

Jazmín

4

Bonjour,

I think medaka 1.4.1 and conda 4.10.1 are now installed, see : Update conda mamba + test medaka (!553) · Merge requests · Institut Français de Bioinformatique / Cluster / tools · GitLab

It have been installed with mamba, which most of time work better than conda.

You can replace conda by mamba on your shell command line, it is availlable on the cluster and it take the same argument and option as conda.

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5

Bonjour,

Indeed, I realized that conda and medaka where updated the lasts days, they work perfectly now. Is good to know about mamba for future references. Thank you!

Jazmin