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AlgoLab / pantas

Differential quantification of alternative splicing events on spliced pangenome graphs
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Hard to install the pantas #2

Open ld9866 opened 1 week ago

ld9866 commented 1 week ago

Dear developer:

We are engaged in the work of pig pangene, and now we want to use pantas to do some analysis of pantranscription, but we find it very difficult to install pantas. I would like to ask if you can provide a docker version, which will be very convenient for the future spread of this software and reduce a lot of trouble in installation.

I also uploaded the problems we encountered, please help us to look at it. Best day! Dong

The code we used: git clone https://github.com/AlgoLab/pantas.git mamba create -c bioconda -c conda-forge -n pantas python=3.10 biopython gffutils intervaltree bcftools samtools gffread vg snakemake-minimal conda activate pantas bash setup.sh setup (2).log

ldenti commented 1 week ago

Hi, sorry for that. We'll look into simplifying pantas installation: docker seems the way to go (thanks for the suggestion). We'll keep you posted.

Best,

ldenti commented 6 days ago

Hi, we are currently working on the docker image. But in the meantime, we should have fixed the compilation errors. If you want, you can try running again bash setup.sh after pulling the new changes. Otherwise, you can wait for the docker image.

Best,