Create an environment from YAML file:
copy seutat.yml file in project folder
inside this folder:
conda env create --file seurat.yml
mkdir bin
mv <path to seurat_tutorial.Rmd>/seurat_tutorial.Rmd ./bin/
mkdir data
cd data
#download data
#The wget option -O specifies a file to which the documents is written, and here we use -, meaning it will written to standard output and piped to tar and the tar #flag -x enables extraction of archive files and -z decompresses, compressed archive files created by gzip
#dataset for tutorial
wget -c https://cf.10xgenomics.com/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz -O - | tar -xz
##for our new dataset, we used the filtered dataset
#wget -c https://cf.10xgenomics.com/samples/cell exp/4.0.0/Targeted_SC3v3_Human_Glioblastoma_Neuroscience/Targeted_SC3v3_Human_Glioblastoma_Neuroscience_raw_feature_bc_matrix.tar.gz -O - | tar -xz
wget -c https://cf.10xgenomics.com/samples/cell-exp/4.0.0/Targeted_SC3v3_Human_Glioblastoma_Neuroscience/Targeted_SC3v3_Human_Glioblastoma_Neuroscience_filtered_feature_bc_matrix.tar.gz -O - | tar -xz
cd ..
mkdir output
cd output
mkdir images
mkdir timings
cd ..
conda activate seurat
rstudio
#which rstudio --- /usr/bin/rstudio
#rstudio -version --- 2021.09.1+372
open seurat_tutorial.Rmd
Maybe you run in troubles, it could be helpful to delete the environment and create again like in step1
conda env remove -n seurat --all
inside the project folder:
mkdir bin
mv <path to seurat_tutorial.Rmd>/seurat_tutorial.Rmd ./bin/
mkdir data
cd data
#download data
#The wget option -O specifies a file to which the documents is written, and here we use -, meaning it will written to standard output and piped to tar and the tar #flag -x enables extraction of archive files and -z decompresses, compressed archive files created by gzip
wget -c https://cf.10xgenomics.com/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz -O - | tar -xz
cd ..
mkdir output
cd output
mkdir images
mkdir timings
cd ..
sudo docker run --rm -d -p 8787:8787 -e PASSWORD=password -v $PWD:/home/rstudio/ seurat
open in your webbrowser:
http://localhost:8787/
Username : rstudio
Password: password
open seurat_tutorial.Rmd
stop running container
sudo docker ps
sudo docker stop <container name>