How to install Ciara on HPC cluster using conda? I tried using conda skeleton, it didnt work about ciara HOT 7 CLOSED

Even though CIARA isn't on conda, it can still be installed through conda from CRAN. Instructions included below for anyone else interested...

conda create --name ciara r-base=4.1.0
conda activate ciara
conda skeleton cran CIARA
sed -i "s/r-biobase$/bioconductor-biobase/" r-ciara/meta.yaml
sed -i "s/r-base$/r-base=4.1.0/" r-ciara/meta.yaml
conda-build r-ciara
conda install --use-local r-ciara

Thanks Gabriele!

from ciara.

For future reference, it's now on conda: https://anaconda.org/kew24/r-ciara
conda install -c kew24 r-ciara

If you prefer that I remove this build from my anaconda channel in favor of you uploading it, let me know!

from ciara.

For installing the python version of CIARA, you can use python -m pip install ciara_python (see here for more info https://github.com/ScialdoneLab/CIARA_python).

from ciara.

Sorry I forgot to mention that is the R version. I need it to run in a cluster. I have to install using conda or something like that but I got this message saying "CIARA is not available on conda channels"

from ciara.

Yes CIARA is not available on conda. You can install R on the cluster, for example with brew install R (https://brew.sh). Once R is installed you can install CIARA with devtools::install_github("ScialdoneLab/CIARA") or the CRAN version with install.packages("CIARA")

from ciara.

There is some problem with R version and Seurat tasks.
I could finally solve this using this tutorial bellow:
https://www.biostars.org/p/498049/

And Finally I could use devtools.

Thanks for your help Gabriel

from ciara.

Perfect 👍, happy that now it works!

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