Linux

Useful Linux Programs with julia

In the Linux terminal:

sudo dpkg --install atom-amd64.deb
sudo apt install ffmpeg
sudo apt-get install cmake bar time binutils make libssl-dev gfortran libunwind8-dev gcc g++ #clang curl perl wget m4 patch pkg-config
sudo apt-get install gsfonts-x11
sudo apt-get install notepadqq
sudo apt-get update
sudo apt-get install gfortran
sudo apt-get install libnlopt0
sudo apt-get install openssh-server
sudo apt install ipmiutil
sudo apt-get install hdf5-tools
apm install latex # Atom package manager for latex!
sudo apt-get install pdf2svg # for PGFPlots
pip install sphinxcontrib-bibtex

Java

First I tried a few things including:

sudo apt-get install default-jre
sudo apt-get update

And:

sudo add-apt-repository ppa:openjdk-r/ppa
sudo apt-get update
sudo apt-get install openjdk-7-jre

This messed stuff up and then I deleted all of my old java versions using:

sudo natilus

Ended up needing to follow this advice <http://askubuntu.com/questions/251213/unable-to-install-default-jdk >:

sudo add-apt-repository ppa:webupd8team/java
sudo apt-get update
sudo apt-get install oracle-java8-installer
java -version
sudo apt-get install oracle-java8-set-default

This finally worked and I was able to run JabRef with no problem using:

java -jar JabRef-3.8.jar

If something is broken:

sudo apt-get -f install

Basic Linux Commands

Never run an executable in root!

Some more info can be found on ` this page <https://www.cyberciti.biz/faq/tar-extract-linux/>`.

To unpack a tar file:

tar -xvf file.tar

To extract a .tar.gz:

tar -xzvf file.tar.gz

Unzip:

unzip stuff.zip -d /destination/folder

directory comment:

$HOME = /home/febbo

Run a jar file: java -jar lad

Issues and Fixes

1. Trying to uninstall sphinx so that I could get a newer version without bugs:

febbo@febbo-HP-ZBook-17-G2:~/Desktop/useful downloads$ pip uninstall sphinx
Cannot remove entries from nonexistent file /home/febbo/anaconda3/lib/python3.5/site-packages/easy-install.pth

The problem: This probably won’t work:

conda update setuptools

The fix, was to download ez_setup.py from this link and run it in the terminal:

febbo@febbo-HP-ZBook-17-G2:~$ python ez_setup.py

Then I could uninstall Sphinx-1.4.1:

febbo@febbo-HP-ZBook-17-G2:~$ pip uninstall sphinx
Uninstalling Sphinx-1.4.1:
/home/febbo/anaconda3/bin/sphinx-apidoc
/home/febbo/anaconda3/bin/sphinx-autogen
/home/febbo/anaconda3/bin/sphinx-build
/home/febbo/anaconda3/bin/sphinx-quickstart
/home/febbo/anaconda3/lib/python3.5/site-packages/Sphinx-1.4.1-py3.5.egg
Proceed (y/n)? y
Successfully uninstalled Sphinx-1.4.1

There was reason I needed to uninstall this version of Sphinx was because the citations where not working.

Finally I installed Sphinx-1.5.2:

#Install from newest dev version in stable branch::
pip install git+https://github.com/sphinx-doc/sphinx@stable