diff --git a/conda_instructions.md b/conda_instructions.md index d96a04cd..0f76c887 100644 --- a/conda_instructions.md +++ b/conda_instructions.md @@ -164,7 +164,7 @@ cd ~/Downloads sh Miniconda3-latest-Linux-x86_64.sh ``` -6. Inside MobaXterm, type the commands below to install the X-server graphical packages that will be used to lauch RStudio. +6. Inside MobaXterm, type the commands below to install the X-server graphical packages that will be used to launch RStudio. [https://docs.anaconda.com/anaconda/install/linux/](https://docs.anaconda.com/anaconda/install/linux/) ``` sudo apt-get update @@ -212,18 +212,26 @@ If by any means you see that the installations are not working as it should on y 6. Proceed with the Ubuntu installation as recommended. You can set to do "Minimal Installation" and deactivate to get updates during installation. -7. Inside UBUNTU, Download conda: + +7. Inside Ubuntu, open TERMINAL and type the commands below to install the X-server graphical packages that will be used to launch RStudio. +[https://docs.anaconda.com/anaconda/install/linux/](https://docs.anaconda.com/anaconda/install/linux/) +``` +sudo apt-get update +sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6 +``` + +8. Inside UBUNTU, Download conda: ``` wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh ``` -8. Inside UBUNTU, open the TERMINAL and type the commands below. Follow the instructions for the installation there. +9. Inside UBUNTU, open the TERMINAL and type the commands below. Follow the instructions for the installation there. ``` cd ~/Downloads sh Miniconda3-latest-Linux-x86_64.sh ``` -9. Close Terminal to apply the CONDA updates. Then you can create a course folder, download the environment file and create the environment: +10. Close Terminal to apply the CONDA updates. Then you can create a course folder, download the environment file and create the environment: ``` mkdir ~/Desktop/course cd ~/Desktop/course @@ -231,7 +239,7 @@ wget https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/e conda env create -n scRNAseq2020 -f environment_r.yml ``` -10. You can then follow the instructions above to activate/deactivate the environment. +11. You can then follow the instructions above to activate/deactivate the environment. ``` conda activate scRNAseq2020 rstudio & diff --git a/exercises.md b/exercises.md index 1216505a..f59ec1b6 100644 --- a/exercises.md +++ b/exercises.md @@ -54,6 +54,15 @@ We highly recommend you to use the files provided instead of copying and pasting
+##### FAQ +*** + +As you run into problems, we will try to fill in the [FAQ](labs/FAQ) with common questions. + +
+ +
+ ##### BONUS exercises *** @@ -78,11 +87,5 @@ We will try to keep these tutorials up to date. If you find any errors or things
-##### FAQ -*** - -As you run into problems, we will try to fill in the [FAQ](labs/FAQ) with common questions. - -
Icons are provided from [www.svgrepo.com](www.svgrepo.com)
diff --git a/labs/FAQ.md b/labs/FAQ.md index 1f9ec897..23fb4f7d 100644 --- a/labs/FAQ.md +++ b/labs/FAQ.md @@ -1,41 +1,56 @@ -# Error - UMAP not found +--- +layout: default +title: 'Precourse Material - scRNAseq course' +--- -If your R does not find the correct python version, it will complain that `umap-learn` is not installed and ask you to install it. Here are some tips on how to find the correct python version that was installed in the conda environment. - -### Try selecting the correct conda env in R: - -In this example the conda env is named `sc_course`. +#### FAQ +*** - library(reticulate) - reticulate:use_conda("sc_course") +
-Then check what python you have in R: - reticulate::py_config() - # should read at top: - python: /Users/asbj/miniconda3/envs/sc_course/bin/python +##### Error - umap-learn not found +*** +If your R does not find the correct python version, it will complain that `umap-learn` is not installed and ask you to install it. Here are some tips on how to find the correct python version that was installed in the conda environment. -If that still is not right, you may have an r-reticulate python installation as well and need to perform the steps below. +**Try selecting the correct conda env in R** -### Restart R and select python version +In this example the conda environment is named `scRNAseq2020`. +``` +library(reticulate) +reticulate::use_conda("scRNAseq2020") +``` -OBS! Before doing anything else you need to select python version. +Then check what python you have in R: +``` +reticulate::py_config() +# should read at top: +python: /Users/asbj/miniconda3/envs/scRNAseq2020/bin/python +``` -First, find out what path you have to your conda python (In terminal): +If that still is not right, you may have an `r-reticulate` python installation as well and need to perform the steps below. - which python - /Users/asbj/miniconda3/envs/sc_course/bin/python +
-Then in R (after restarting): +**Restart R and select python version** - reticulate::use_python("/Users/asbj/miniconda3/envs/sc_course/bin/python", required=T) +OBS! Before doing anything else you need to select python version. +First, find out what path you have to your conda python (in TERMINAL): +``` +which python +/Users/asbj/miniconda3/envs/scRNAseq2020/bin/python +``` -Then check again with py_config if correct version of python is used: +Then in R (after restarting): +``` +reticulate::use_python("/Users/asbj/miniconda3/envs/scRNAseq2020/bin/python", required=T) +``` - reticulate::py_config() +Then check again with `py_config` if correct version of python is used: +``` +reticulate::py_config() +``` If you have the correct version now, you should be able to run UMAP without issues. - -