Create notes_cellxgene.md

notes_cellxgene.md

@@ -0,0 +1,66 @@
+# Notes for installing cellxgene
+
+[cellxgene](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/README.md) is an interactive browser for single-cell data that is being developed by the CZI.
+
+* Tutorials for [exploring data using cellxgene](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/explore-data/explorer-tutorials.md)
+* [CZI's install help](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/install.md) -- this only installs the basic cellxgene browser -- we typically prefer to install it along with the [VIP tools](https://github.com/interactivereport/cellxgene_VIP) that allow for violin plots and more
+* [collection of browsable public data sets](https://cellxgene.cziscience.com/)
+
+Pre-requisites **on MacOS** are:
+
+* **command line tools installed?**
+  - if NOT, run `xcode-select --install` in the Terminal
+* **conda installed?**
+  - if NOT, do that first; see <https://docs.conda.io/projects/continuumio-conda/en/latest/user-guide/install/macos.html>
+
+  ```
+  curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O Miniconda3-latest-MacOSX-x86_64.sh
+  bash Miniconda3-latest-MacOSX-x86_64.sh
+  ### AFTER YOU INSTALL CONDA, RESTART THE TERMINAL! ####
+  ```
+
+* **R installed?**
+ - if NOT, install R: download <https://cran.r-project.org/bin/macosx/base/R-4.0.4.pkg> and follow instructions  
+
+Then, let's brace yourself for cellxgene VIP:
+
+```
+## cellxgene  VIP install
+git clone https://github.com/interactivereport/cellxgene_VIP.git
+cd cellxgene_VIP
+#conda config --set channel_priority flexible
+conda env create -n VIP -f VIP.macOS.yml
+conda activate VIP
+./config.macOS.sh
+export LIBARROW_MINIMAL=false
+#  ensure that the right instance of R is used.
+# e.g. system-wide: /bin/R or /usr/bin/R ;
+# local R under conda: ~/.conda/envs/VIP_conda_R/bin/R
+which R
+## DO CAIRO BEFORE ALL ELSE 
+conda install -c anaconda cairo 
+conda install -c conda-forge cairo 
+
+# open R
+R
+install.packages(c("devtools", "Cairo", "foreign", "ggpubr", "ggrastr", "arrow", "Seurat", "rmarkdown", "tidyverse", "viridis", "BiocManager"), type="binary")
+BiocManager::install("fgsea")
+
+# quit R 
+R -q -e 'if(!require(dbplyr)) devtools::install_version("dbplyr",version="1.0.2",repos = "http://cran.us.r-project.org")'
+R -q -e 'if(!require(RColorBrewer)) devtools::install_version("RColorBrewer",version="1.1-2",repos = "http://cran.us.r-project.org")'
+R -q -e 'if(!require(glue)) devtools::install_version("glue",version="1.4.2",repos = "http://cran.us.r-project.org")'
+R -q -e 'if(!require(gridExtra)) devtools::install_version("gridExtra",version="2.3",repos = "http://cran.us.r-project.org")'
+R -q -e 'if(!require(ggrepel)) devtools::install_version("ggrepel",version="0.8.2",repos = "http://cran.us.r-project.org")'
+R -q -e 'if(!require(MASS)) devtools::install_version("MASS",version="7.3-51.6",repos = "http://cran.us.r-project.org")'
+R -q -e 'if(!require(data.table)) devtools::install_version("data.table",version="1.13.0",repos = "http://cran.us.r-project.org")'
+
+ps -ef | grep cellxgene
+Rscript -e 'reticulate::py_config()'
+# Run the following command if the output of the above command doesn't point to the Python in your env.
+export RETICULATE_PYTHON=`which python`
+cellxgene launch our_data.h5ad
+
+conda activate VIP
+cellxgene launch our_data.h5ad
+```