adds more explanation on exercises

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
@@ -212,26 +212,34 @@ 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
 wget https://raw.githubusercontent.com/NBISweden/workshop-scRNAseq/master/labs/environment_r.yml
 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 &

exercises.md

@@ -54,6 +54,15 @@ We highly recommend you to use the files provided instead of copying and pasting
 
 <br/>
 
+##### <img border="0" src="https://www.svgrepo.com/show/83019/faq-button.svg" width="40" height="40"> FAQ
+***
+
+As you run into problems, we will try to fill in the [FAQ](labs/FAQ) with common questions.
+
+<br/>
+
+<br/>
+
 ##### <img border="0" src="https://www.svgrepo.com/show/759/exercise.svg" width="40" height="40"> BONUS exercises
 ***
 
@@ -78,11 +87,5 @@ We will try to keep these tutorials up to date. If you find any errors or things
 
 <br/>
 
-##### <img border="0" src="https://www.svgrepo.com/show/83019/faq-button.svg" width="40" height="40"> FAQ
-***
-
-As you run into problems, we will try to fill in the [FAQ](labs/FAQ) with common questions.
-
-<br/>
 
 <div style="text-align: right; font-size: 5px"> Icons are provided from [www.svgrepo.com](www.svgrepo.com) </div>

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`.
+#### <img border="0" src="https://www.svgrepo.com/show/83019/faq-button.svg" width="40" height="40"> FAQ
+***
 
-      library(reticulate)
-      reticulate:use_conda("sc_course")
+<br/>
 
-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
+<br/>
 
-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.
-
-