Steps for installing Anaconda and associated open source packages

2018-12-04 Last updated by Adam Lu

Download the installation bash script to:
~/Software/Anaconda3-5.1.0-Linux-x86_64.sh or ~/Software/Anaconda3-5.2.0-Linux-x86_64.sh
Check the md5sum against values here or here:

  md5sum ~/Software/Anaconda3-5.1.0-Linux-x86_64.sh
  md5sum ~/Software/Anaconda3-5.2.0-Linux-x86_64.sh

Install Anaconda:

  sudo bash /home/adam/Software/Anaconda3-5.2.0-Linux-x86_64.sh

+ When prompted for where to install, choose this:      **`/opt/anaconda3`** (the `/opt` directory is accessible to all users)

Change the $PATH environmental variable in login shells
- Method 1 (preferred): Add the following line to the file /etc/bash.bashrc:
```
export PATH="$PATH:/opt/anaconda3/bin"
```
  This will edit the environmental variable $PATH for all users. This is preferred over editing the /etc/environment file.
- Method 2 (not preferred): Add /opt/anaconda3/bin to the first line of the file /etc/environment:
```
PATH="/opt/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games"
```
  However, before logging out and logging back in, one would need to place the following in the ~/.bashrc file:
```
export PATH="/opt/anaconda3/bin:$PATH"
```
Change the permissions so that anaconda can be updated and other packages can be installed:

  sudo chown -R adam:LabFolks /opt/anaconda3
  sudo chmod -R 775 /opt/anaconda3

Update Anaconda:

  conda update -n base conda

Install the Anaconda compiler tools:

  # Install the C compiler
  conda install gcc_linux-64
  
  # Install the C++ compiler
  conda install gxx_linux-64
  
  # Install the FORTRAN compiler
  conda install gfortran_linux-64

Install the GNU Scientific library:

  # Install just the library
  # sudo apt-get install libgsl0ldbl (obsolete?)
  sudo apt-get install libgsl23
  
  # Install the development package and binary
  # sudo apt-get install gsl-bin libgsl0-dev
  sudo apt-get install gsl-bin libgsl-dev
  
  # Install the resources/documentations
  sudo apt-get install gsl-doc-info gsl-doc-pdf gsl-ref-html gsl-ref-psdoc
  
  # Install GSL within conda
  conda install gsl

Install RStudio:

  # Install Rstudio from the R channel
  conda install -c r rstudio 

Install other R packages through Anaconda:

  # Install all packages from tidyverse (includes dplyr, readr, etc.)
  conda install -c r r-tidyverse
  
  # Install all packages in r-essentials
  conda install -c r r-essentials

  # TODO: Does not work: Install the R wrapper for the GNU scientific library
  conda install -c r r-gsl

  # Update all associated packages
  conda update --all

Within RStudio, install libraries to the Anaconda path:

# For swirl tutorials
install.packages("swirl", "/opt/anaconda3/lib/R/library")

# For bee-swarm plots that work with ggplot2
install.packages("ggbeeswarm", "/opt/anaconda3/lib/R/library")
    
# For themes that work with ggplot2
install.packages("ggthemes", "/opt/anaconda3/lib/R/library")

# For area under the curve (AUC) and more
install.packages("DescTools", "/opt/anaconda3/lib/R/library")

# TODO: Does not work: For PearsonDS
install.packages("gsl", "/opt/anaconda3/lib/R/library")    

# For Pearson distributions
install.packages("PearsonDS", "/opt/anaconda3/lib/R/library")

# For 
install.packages("kableExtra", "/opt/anaconda3/lib/R/library")    

# For 
install.packages("googledrive", "/opt/anaconda3/lib/R/library")    

# For 
install.packages("R.utils", "/opt/anaconda3/lib/R/library")    

# For 
install.packages("plot3D", "/opt/anaconda3/lib/R/library")    

Install TeX Live:
```bash # For most LaTeX packages sudo apt-get install texlive

# For the titling package sudo apt-get install texlive-latex-extra

12. Install other Python tools
    * [**Bokeh**](https://bokeh.pydata.org/):  
      ```bash
      conda install bokeh
      ```
    * [**Rise**](https://anaconda.org/damianavila82/rise) (slideshows):  
      ```bash
      conda install -c damianavila82 rise
      ```

    - Required for the `cv2` package (not working on fishfish)
    
        ```bash
        conda install -c https://conda.binstar.org/menpo opencv
        ```
    
13. Create desktop shortcuts:

    * To place in **Applications Menu**, copy the **.desktop** files to `/usr/share/applications/`:

      ```bash
      cp -p ~/Settings_Anaconda/spyder3.desktop /usr/share/applications/
      cp -p ~/Settings_Anaconda/rstudio.desktop /usr/share/applications/
      ```

    * To create a **desktop shortcut**, copy the **.desktop** files to `/home/${user}/Desktop`:

      ```bash
      cp -p ~/Settings_Anaconda/spyder3.desktop ~/Desktop/
      cp -p ~/Settings_Anaconda/rstudio.desktop ~/Desktop/
      ```

    * Or run the bash scripts:

      ```bash
      /media/adamX/Settings_Linux/setup_desktopfiles.sh
      /media/adamX/Settings_Linux/setup_all_desktopfiles.sh
      ```

14. The man command stopped working do to an incorrect link for `/opt/anaconda/bin/pager`
    * Issue: See this [link](https://askubuntu.com/questions/623992/what-is-the-default-pager-used-by-man-pages).
    * Workaround (note: different from that provided by the link):

      ```bash
      # Backup the default link to pager
      mv /opt/anaconda3/bin/pager /opt/anaconda3/bin/pager-backup
      
      # Create a new link to original pager
      ln -s /usr/bin/pager /opt/anaconda3/bin/pager
      ```

15. Spyder3 and Anaconda Navigator ran into **segfault**

    - Issue: See this [link](https://github.com/spyder-ide/spyder/issues/6968).

    - Workaround:

      ```bash
      # Downgrade PyQT to version 5.6
      conda install pyqt==5.6
      ```

16. Installed **[Open CV](https://opencv.org/)**:

    - Followed [these instructions](https://anaconda.org/conda-forge/opencv), after following [these instructions](https://docs.opencv.org/3.4.1/d2/de6/tutorial_py_setup_in_ubuntu.html) (which was probably unnecessary). Typed these commands in a terminal:

      ```bash
      # Install Open CV for Python through Anaconda
      conda install -c conda-forge opencv
      conda install -c conda-forge/label/broken opencv
      
      # Install Open CV for Python (obsolete)
      sudo apt-get install python-opencv
      
      # Install Open CV documentation and data (obsolete)
      sudo apt-get install opencv*
      ```

***

#### Old versions:

- Done on earlier versions of Ubuntu:

  * Within RStudio, install the [**DescTools** library](https://www.rdocumentation.org/packages/DescTools/versions/0.99.19) (for `AUC()`): (Didn't work for Ubuntu 18!)

    ```R
    install.packages("DescTools")
    ```

  * Install the [**gsl** library](https://www.rdocumentation.org/packages/gsl/versions/2.1-1) (R wrapper for the GNU Scientific library):  (Didn't work for Ubuntu 18!)
    ```R
    install.packages("gsl")
    ```
  * Install the [**PearsonDS** library](https://www.rdocumentation.org/packages/PearsonDS/versions/0.97) (for Pearson distributions):  (Didn't work for Ubuntu 18!)
    ```R
    install.packages("c")
    ```

- Attempted on 2018-12-04

  ```bash
  # Removed packages that I thought to have interfered with r-ggbeeswarm,  r-pearsonds && r-ggthemes  
  conda remove -c r r-microsoftr
  conda remove -c r r-revoioq
  conda remove -c r r-deployrrserve
  conda remove -c r r-revoutilsmath

  # Re-installed r-essentials
  conda install -c r r-essentials

  # These did not work
  conda install -c conda-forge r-ggbeeswarm
  conda install -c conda-forge r-ggthemes
  conda install -c cramjaco r-pearsonds  