Conda package

[Zethson]

Hi,

would it be possible that you add nichenet to Bioconda?

Thank you very much

[browaeysrobin]

Hi @Zethson

I will have a look into this.

[ejc043]

Is there any update on the conda implementation?

[browaeysrobin]

@ejc043
Because of multiple projects and lack of time, this is currently not one of my main priorities (this can change if you can convince me that adding it to Bioconda could be very beneficial).

[akiss-me]

@ejc043 Because of multiple projects and lack of time, this is currently not one of my main priorities (this can change if you can convince me that adding it to Bioconda could be very beneficial).

Today I spent 5 hours on the installation of nichenet, conda could help save time for installation.

[akiss-me]

This is the code for nichenet installation in conda enviroment:

conda install -c conda-forge -c bioconda -c defaults r-essentials r-remotes geos cmake -y
&& R -e 'options(Ncpus = 4); install.packages(c("BiocManager", "rstatix", "Seurat"), repos="https://mirror.truenetwork.ru/CRAN/"); q()'
&& R -e 'BiocManager::install(c("ComplexHeatmap", "limma", )); q()'
&& R -e 'remotes::install_github("saeyslab/nichenetr", upgrade = "always"); q()'

[sfortma2]

@ejc043 Because of multiple projects and lack of time, this is currently not one of my main priorities (this can change if you can convince me that adding it to Bioconda could be very beneficial).

Today I spent 5 hours on the installation of nichenet, conda could help save time for installation.

Yup, same here. Took me 2 days of on and off attempts to get a working conda environment for NicheNet. Love the software though!

[shufanzhang]

It also take me half day to install this package in micromamba, R4.0.0 can not install successful for that some package rely on R>4.1. My R version is 4.2.3. Here is my successful install：

#build a clean environment:
micromamba create -y -n CCI
micromamba activate CCI

#install R-base and packages that can not be installed by devtools::install_github:
micromamba install -c bioconda -c conda-forge r-base r-devtools
bioconductor-limma r-hmisc r-randomforest r-mlrmbo r-ggpubr bioconductor-complexheatmap

#run this in R:
devtools::install_github("saeyslab/nichenetr")

[Elo-mars]

It also take me half day to install this package in micromamba, R4.0.0 can not install successful for that some package rely on R>4.1. My R version is 4.2.3. Here is my successful install：

#build a clean environment: micromamba create -y -n CCI micromamba activate CCI

#install R-base and packages that can not be installed by devtools::install_github: micromamba install -c bioconda -c conda-forge r-base r-devtools bioconductor-limma r-hmisc r-randomforest r-mlrmbo r-ggpubr bioconductor-complexheatmap

#run this in R: devtools::install_github("saeyslab/nichenetr")

For conda users, and a bit of an update from November 2023 (and after 4 hours of trying??)

this works for me:

conda create --name MN python=3.12
conda activate MN

conda install -c conda-forge r-base
conda install -c conda-forge r-seurat
conda install -c bioconda bioconductor-singlecellexperiment
conda install -c conda-forge r-dplyr
conda install -c conda-forge r-ggplot2
conda install -c bioconda -c conda-forge r-base r-devtools
conda install  bioconductor-limma r-hmisc r-randomforest r-mlrmbo r-ggpubr bioconductor-complexheatmap
conda install -c conda-forge r-caret
conda install -c conda-forge r-ggforce
conda install -c conda-forge r-rspectra r-rcpphnsw

R
devtools::install_github("saeyslab/nichenetr") # with warnings

conda install -c bioconda bioconductor-muscat bioconductor-scater bioconductor-edger bioconductor-sva bioconductor-scran
conda install -c conda-forge r-ggraph

devtools::install_github("saeyslab/multinichenetr")

but thanks for the package, it's wonderful :)